1
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Monu, Oram BK, Bandyopadhyay B. Revisiting the IR Spectra of H 2S in an Argon Matrix: Identification of (H 2S) n ( n ≤ 4) Clusters via the Spectral Assignment of νS-H Transitions. J Phys Chem A 2024. [PMID: 39101267 DOI: 10.1021/acs.jpca.4c04025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/06/2024]
Abstract
Small-molecular clusters of H2S up to tetramer have been experimentally identified in a cold and solid argon matrix by the spectral assignment of νS-H fundamental transitions for different H2S:argon mixing ratios. Normal-mode frequency calculations at the MP2-CP/aug-cc-pV(Q + d)Z level have been used to support the spectral assignments. In addition, modulations in relative populations of different clusters due to the annealing of the deposited matrix and the preheating of the H2S-argon gas mixture before deposition reinforced the spectral assignments. Variations in mixing ratio, annealing of the matrix, and preheating of the gas mixture have also been used, in a combined manner, to unambiguously identify the ν1 and ν3 bands of the H2S monomer, which has been a matter of dispute for a long period. The two bands have been identified at 2634.4 and 2648.0 cm-1, respectively, while three bands at 2581.5, 2568.4, and 2547.6 cm-1 have been assigned to H-bonded dimers, cyclic trimers, and cyclic tetramers, respectively. Multiple bands within 2550-2580 cm-1 have been assigned to caged tetramers. The cooperative strengthening of S-H···S H bonds in cyclic H2S clusters was evident from the linear increment in νS-H spectral shifts with cluster size.
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Affiliation(s)
- Monu
- Department of Chemistry, Malaviya National Institute of Technology Jaipur, J L N Marg, Jaipur 302017, India
| | - Binod Kumar Oram
- Department of Chemistry, Malaviya National Institute of Technology Jaipur, J L N Marg, Jaipur 302017, India
| | - Biman Bandyopadhyay
- Department of Chemistry, Malaviya National Institute of Technology Jaipur, J L N Marg, Jaipur 302017, India
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2
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Burevschi E, Chrayteh M, Murugachandran SI, Loru D, Dréan P, Sanz ME. Water Arrangements upon Interaction with a Rigid Solute: Multiconfigurational Fenchone-(H 2O) 4-7 Hydrates. J Am Chem Soc 2024; 146:10925-10933. [PMID: 38588470 PMCID: PMC11027134 DOI: 10.1021/jacs.4c01891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 03/19/2024] [Accepted: 03/20/2024] [Indexed: 04/10/2024]
Abstract
Insight into the arrangements of water molecules around solutes is important to understand how solvation proceeds and to build reliable models to describe water-solute interactions. We report the stepwise solvation of fenchone, a biogenic ketone, with 4-7 water molecules. Multiple hydrates were observed using broadband rotational spectroscopy, and the configurations of four fenchone-(H2O)4, three fenchone-(H2O)5, two fenchone-(H2O)6, and one fenchone-(H2O)7 complexes were characterized from the analysis of their rotational spectra in combination with quantum-chemical calculations. Interactions with fenchone deeply perturb water configurations compared with the pure water tetramer and pentamer. In two fenchone-(H2O)4 complexes, the water tetramer adopts completely new arrangements, and in fenchone-(H2O)5, the water pentamer is no longer close to being planar. The water hexamer interacts with fenchone as the least abundant book isomer, while the water heptamer adopts a distorted prism structure, which forms a water cube when including the fenchone oxygen in the hydrogen bonding network. Differences in hydrogen bonding networks compared with those of pure water clusters show the influence of fenchone's topology. Specifically, all observed hydrates except one show two water molecules binding to fenchone through each oxygen lone pair. The observation of several water arrangements for fenchone-(H2O)4-7 complexes highlights water adaptability and provides insight into the solvation process.
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Affiliation(s)
| | - Mhamad Chrayteh
- PhLAM—Physique
des Lasers, Atomes et Molécules, University of Lille, CNRS, UMR 8523, F-59000 Lille, France
| | | | - Donatella Loru
- Department
of Chemistry, King’s College London, London SE1 1DB, U.K.
| | - Pascal Dréan
- PhLAM—Physique
des Lasers, Atomes et Molécules, University of Lille, CNRS, UMR 8523, F-59000 Lille, France
| | - M. Eugenia Sanz
- Department
of Chemistry, King’s College London, London SE1 1DB, U.K.
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3
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Rock CA, Tschumper GS. Insight into the Binding of Argon to Cyclic Water Clusters from Symmetry-Adapted Perturbation Theory. Int J Mol Sci 2023; 24:17480. [PMID: 38139311 PMCID: PMC10744083 DOI: 10.3390/ijms242417480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 12/06/2023] [Accepted: 12/07/2023] [Indexed: 12/24/2023] Open
Abstract
This work systematically examines the interactions between a single argon atom and the edges and faces of cyclic H2O clusters containing three-five water molecules (Ar(H2O)n=3-5). Full geometry optimizations and subsequent harmonic vibrational frequency computations were performed using MP2 with a triple-ζ correlation consistent basis set augmented with diffuse functions on the heavy atoms (cc-pVTZ for H and aug-cc-pVTZ for O and Ar; denoted as haTZ). Optimized structures and harmonic vibrational frequencies were also obtained with the two-body-many-body (2b:Mb) and three-body-many-body (3b:Mb) techniques; here, high-level CCSD(T) computations capture up through the two-body or three-body contributions from the many-body expansion, respectively, while less demanding MP2 computations recover all higher-order contributions. Five unique stationary points have been identified in which Ar binds to the cyclic water trimer, along with four for (H2O)4 and three for (H2O)5. To the best of our knowledge, eleven of these twelve structures have been characterized here for the first time. Ar consistently binds more strongly to the faces than the edges of the cyclic (H2O)n clusters, by as much as a factor of two. The 3b:Mb electronic energies computed with the haTZ basis set indicate that Ar binds to the faces of the water clusters by at least 3 kJ mol-1 and by nearly 6 kJ mol-1 for one Ar(H2O)5 complex. An analysis of the interaction energies for the different binding motifs based on symmetry-adapted perturbation theory (SAPT) indicates that dispersion interactions are primarily responsible for the observed trends. The binding of a single Ar atom to a face of these cyclic water clusters can induce perturbations to the harmonic vibrational frequencies on the order of 5 cm-1 for some hydrogen-bonded OH stretching frequencies.
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Affiliation(s)
| | - Gregory S. Tschumper
- Department of Chemistry and Biochemistry, University of Mississippi, University, MS 38677-1848, USA
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4
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Harold SE, Warf SL, Shields GC. Prebiotic dimer and trimer peptide formation in gas-phase atmospheric nanoclusters of water. Phys Chem Chem Phys 2023; 25:28517-28532. [PMID: 37847315 DOI: 10.1039/d3cp02915h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2023]
Abstract
Insight into the origin of prebiotic molecules is key to our understanding of how living systems evolved into the complex network of biological processes on Earth. By modelling diglycine and triglycine peptide formation in the prebiotic atmosphere, we provide a plausible pathway for peptide growth. By examining different transition states (TSs), we conclude that the formation of diglycine and triglycine in atmospheric nanoclusters of water in the prebiotic atmosphere kinetically favors peptide growth by an N-to-C synthesis of glycines through a trans conformation. Addition of water stabilizes the TS structures and lowers the Gibbs free activation energies. At temperatures that model the prebiotic atmosphere, the free energies of activation with a six water nanocluster as part of the TS are predicted to be 16 kcal mol-1 relative to the prereactive complex. Examination of the trans vs. cis six water transition states reveals that a homodromic water network that maximizes the acceptor/donor nature of the six waters is responsible for enhanced kinetic favorability of the trans N-to-C pathway. Compared to the non-hydrated trans TS, the trans six-water TS accelerates the reaction of diglycine and glycine to form triglycine by 13 orders of magnitude at 217 K. Nature uses the trans N-to-C pathway to synthesize proteins in the ribosome, and we note the similarities in hydrogen bond stabilization between the transition state for peptide synthesis in the ribosome and the transition states formed in nanoclusters of water in the same pathway. These results support the hypothesis that small oligomers formed in the prebiotic atmosphere and rained onto earth's surface.
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Affiliation(s)
- Shannon E Harold
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, USA.
| | - Skyler L Warf
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, USA.
| | - George C Shields
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, USA.
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5
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Bready CJ, Vanovac S, Odbadrakh TT, Shields GC. Amino Acids Compete with Ammonia in Sulfuric Acid-Based Atmospheric Aerosol Prenucleation: The Case of Glycine and Serine. J Phys Chem A 2022; 126:5195-5206. [PMID: 35896016 DOI: 10.1021/acs.jpca.2c03539] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We present a computational investigation of the sulfuric acid, glycine, serine, ammonia, and water system to understand if this system can form prenucleation clusters, which are precursors to larger aerosols in the atmosphere. We have performed a comprehensive configurational search of all possible clusters in this system, starting with the four different monomers and zero to five waters. Accurate Gibbs free energies of formation have been calculated with the DLPNO-CCSD(T)/complete basis set (CBS) method on ωb97xd/6-31++G** geometries. For the dry dimers of sulfuric acid, the weakest base, serine, is found to form the most stable complex, which is a consequence of the strong di-ionic complex formed between the bisulfate ion and the protonated serine cation. For the dry dimers without sulfuric acid, the glycine-serine complex is more stable than the glycine-ammonia or serine-ammonia complexes, stemming from the detailed structure and not related to base strength. For the larger complexes, sulfuric acid deprotonates and the proton is shifted to glycine, serine, or ammonia. The two amino acids and ammonia are almost interchangeable and there is no easy way to predict which molecule will be protonated without the calculated results. Assuming reasonable starting concentrations and a closed system of sulfuric acid, glycine, serine, ammonia, and five waters, we predict the concentrations of all possible complexes at two temperatures spanning the troposphere. The most negative ΔG° values are a function of the detailed molecular interactions of these clusters. These details are more important than the base strength of ammonia, glycine, and serine.
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Affiliation(s)
- Conor J Bready
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, United States
| | - Sara Vanovac
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, United States
| | - Tuguldur T Odbadrakh
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, United States
| | - George C Shields
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, United States
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6
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Mohaček-Grošev V, Furić K, Vujnović V. Raman study of water deposited in solid argon matrix. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 269:120770. [PMID: 34954478 DOI: 10.1016/j.saa.2021.120770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Revised: 12/06/2021] [Accepted: 12/12/2021] [Indexed: 06/14/2023]
Abstract
New Raman data are presented concerning H2O and D2O water aggregation in argon matrix having the ratio of number of argon atoms to water molecules close to 40:1. Experiments were conducted at temperatures from 8 K to 34 K allowing observation of OH and OD stretching vibrations of water monomers, dimers, trimers and higher multimers, as well as broad bands corresponding to solid amorphous water. Molecular dynamics simulations were performed for thirteen or sometimes fourteen water molecules dispersed among 500 argon atoms. Resulting final configurations included dimers, trimers, tetramers and pentamers, all in open chain configurations which upon optimization resulted in mostly cyclic conformations. Observed OH stretching vibrations were assigned by comparing calculated normal modes in harmonic approximation at the B3LYP/aug-cc-pVDZ and PBEPBE1/aug-cc-pVDZ level of theory with our data and previously observed bands from infrared matrix isolation studies and Raman jet cooled experiments. Raman bands assigned to water multimers in argon matrix are shifted 20 to 25 cm-1 towards lower wavenumbers with respect to the positions of OH stretching vibrations of almost free water clusters.
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Affiliation(s)
- Vlasta Mohaček-Grošev
- Center of Excellence for Advanced Materials and Sensing Devices, Research Unit New Functional Materials, Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia.
| | - Krešimir Furić
- Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia
| | - Vedran Vujnović
- Department of Physics and Centre for Micro- and Nanosciences and Technologies, University of Rijeka, Radmile Matejčić 2, 51000 Rijeka, Croatia.
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7
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Xu S, Wu L, Li Z. Nucleation of Water Clusters in Gas Phase: A Computational Study Based on Neural Network Potential and Enhanced Sampling ※. ACTA CHIMICA SINICA 2022. [DOI: 10.6023/a22010003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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8
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Monu, Oram BK, Bandyopadhyay B. A unified cost-effective method for the construction of reliable potential energy surfaces for H 2S and H 2O clusters. Phys Chem Chem Phys 2021; 23:18044-18057. [PMID: 34387290 DOI: 10.1039/d1cp01544c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A DFT-based methodology has been used to construct the potential energy surface of H2S clusters up to pentamers. Geometrical parameters and energetics show very good agreement with the existing experimental and high-level theoretical results. Distinct stable conformers of three dimers, six trimers, eleven tetramers and twenty-three pentamers have been identified. Both S-HS H-bond and SS interactions are identified in dimers, trimers and pentamers, while no SS interactions could be found in any of the 11 tetramer conformers. The binding energies of the most stable dimer, trimer, tetramer and pentamer are -1.66, -5.21, -8.57 and -12.54 kcal mol-1, respectively. The PES has been found to be exceedingly flat and the energy gap between the most and the least stable conformers was found to be only 0.09, 2.13, 1.65 and 1.13 kcal mol-1, from the dimer to the pentamer, respectively. The proposed method has also been used for water clusters up to the pentamer. The results obtained were found to agree closely with the existing results. Only one conformer was found for the water dimer, whereas four, five and fifteen conformers were obtained for the trimer, tetramer and pentamer, respectively. Atoms in molecular calculations were found to corroborate with the geometric and energetic results for both clusters.
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Affiliation(s)
- Monu
- Department of Chemistry, Malaviya National Institute of Technology Jaipur, JLN Marg, Jaipur - 302017, India.
| | - Binod Kumar Oram
- Department of Chemistry, Malaviya National Institute of Technology Jaipur, JLN Marg, Jaipur - 302017, India.
| | - Biman Bandyopadhyay
- Department of Chemistry, Malaviya National Institute of Technology Jaipur, JLN Marg, Jaipur - 302017, India.
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9
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Li Y, Siddique F, Aquino AJA, Lischka H. Molecular Dynamics Simulation of the Excited-State Proton Transfer Mechanism in 3-Hydroxyflavone Using Explicit Hydration Models. J Phys Chem A 2021; 125:5765-5778. [PMID: 34165983 DOI: 10.1021/acs.jpca.1c03687] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
3-Hydroxyflavon (3-HF) represents an interesting paradigmatic compound to study excited-state intramolecular proton transfer (ESIPT) and intermolecular (ESInterPT) processes to explain the experimentally observed dual fluorescence in solvents containing protic contamination (water) as opposed to single fluorescence in highly purified nonpolar solvents. In this work, adiabatic on-the-fly molecular dynamics simulations have been performed for isolated 3-HF in an aqueous solution using a polarizable continuum model and including explicit water molecules to represent adequately hydrogen bonding. For the calculation of the excited state, time-dependent density functional theory and the Becke-3-Lee-Yang-Parr (B3LYP) functional have been used. For the isolated 3-HF, ultrafast ESIPT from the enol group to the neighboring keto group has been observed. The calculated PT time of 48 fs agrees well with the experimental value of 39 fs. Addition of one water molecule quenches this ESIPT process but shows an intermolecular concerted or stepwise tautomerization process via the bridging water molecule. Adding a second or more water molecules inhibits this ESInterPT process to a large degree. Most of the trajectories do not show any PT, preserving the initial excited-state enol structure, which is the origin of the violet-blue fluorescence appearing in the solvents contaminated with protic components.
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Affiliation(s)
- Yingchao Li
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, P. R. China
| | - Farhan Siddique
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, P. R. China
| | - Adélia J A Aquino
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, P. R. China.,Department of Mechanical Engineering, Texas Tech University, Lubbock, Texas 79409, United States
| | - Hans Lischka
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, P. R. China.,Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, United States
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10
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Stabilization of Near Identical Hydrogen Bonded Octameric Water Clusters in Crystal Structures of Three Distinct Non-Charged Polyamide Macrocyclic Host Molecules. Molecules 2021; 26:molecules26092787. [PMID: 34065060 PMCID: PMC8125911 DOI: 10.3390/molecules26092787] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 04/27/2021] [Accepted: 05/06/2021] [Indexed: 11/16/2022] Open
Abstract
In this paper, we present a comparative analysis of the solid state structures of three well-resolved hydrates of macrocyclic host molecules 1a, 1b, and 2 containing an intrannular amide-aryl substituent (lariat arm) connected to a fixed 26-membered ring in a normal (-NHCOAr, hosts 1a and 1b) or reverse manner (-CONHAr, host 2). Despite different chemical structures, these hosts crystallize as isostructural tetrahydrates in the same P-1 space group. Moreover, their crystals exhibit identical hydrogen bond motifs resulting in a stabilization of an almost identical unusual octameric water cluster built from the cyclic tetramer core and four water molecules, attached sequentially in an "up-and-down" manner. Further analysis reveals that, among the series, the structure of host 2 provides the most suitable environment for the accommodation of this type of water cluster.
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11
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Gale AG, Odbadrakh TT, Ball BT, Shields GC. Water-Mediated Peptide Bond Formation in the Gas Phase: A Model Prebiotic Reaction. J Phys Chem A 2020; 124:4150-4159. [DOI: 10.1021/acs.jpca.0c02906] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ariel G. Gale
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, United States
| | - Tuguldur T. Odbadrakh
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, United States
| | - Benjamin T. Ball
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, United States
| | - George C. Shields
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, United States
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12
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Samala NR, Agmon N. Temperature Dependence of Intramolecular Vibrational Bands in Small Water Clusters. J Phys Chem B 2019; 123:9428-9442. [PMID: 31553613 DOI: 10.1021/acs.jpcb.9b07777] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Cyclic water clusters are pivotal for understanding atmospheric reactions as well as liquid water, yet the temperature (T) dependence of their dynamics and spectroscopy is poorly studied. The development of highly accurate water potentials, such as MB-pol, partly rectifies this. It remains to account for the quantum nuclear effects (NQE), because quantum nuclear dynamics become increasingly inaccurate at low temperatures. From a practical point of view, we find that NQE can be accounted for simply by subtracting a constant from the frequencies obtained from the velocity autocorrelation functions (VACF) of classical nuclear dynamics, resulting in unprecedented agreement with experiment, mostly within 5 cm-1. We have performed classical simulations of (H2O)n clusters (n = 2-5) from 20 K and up to their melting temperature, calculating both all-atom and partial VACF, thus generating the temperature dependence of the vibrational frequencies (IR and Raman bands). Focusing on the hydrogen-bonded (HBed) OH stretch and HOH bend, we find opposing T dependencies. The HBed OH modes blue shift linearly with T, attributed to ring expansion rather than any specific conformational change. The lowest-frequency Raman concerted mode is predicted to show the largest such shift. In contrast, the HOH bend undergoes a red-shift, with the highest frequency concerted band undergoing the largest red-shift. These results can be explained by a coupled-oscillator model for n hydrogen atoms on a ring, constrained to move either tangentially (stretch) or perpendicularly (bend) to the ring. With increasing temperature and weakening of HBs, the intrinsic force constant increases (stretch) or remains constant (bend), while the nearest-neighbor coupling constant decreases, and this results in the interesting behavior revealed herein. T-dependent Raman studies are required for testing some of these predictions.
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Affiliation(s)
- Nagaprasad Reddy Samala
- The Fritz Haber Research Center, Institute of Chemistry , The Hebrew University of Jerusalem , Jerusalem 91904 , Israel
| | - Noam Agmon
- The Fritz Haber Research Center, Institute of Chemistry , The Hebrew University of Jerusalem , Jerusalem 91904 , Israel
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13
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Gregory N, Reveles JU, Bly J, Luong T. Ab Initio Molecular Dynamics Investigation of the Electronic and Structural Stability of Anionic O 2-(H 2O) n, n = 1-16 Clusters. J Phys Chem A 2019; 123:7528-7535. [PMID: 31387356 DOI: 10.1021/acs.jpca.9b04510] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report an ab initio molecular dynamics investigation of the electronic and structural stability of water molecules binding to a nucleation O2- particle, O2-(H2O)n with n = 1-16, to ascertain the factors that create particularly stable species. Our results compare well with previous experimental and theoretical reports for clusters with less water content, find three new geometries for species with 7, 9, and 10 water molecules, and determine that 8, 11, 13, and 15 water molecules form remarkably stable structures around O2-. These special clusters correspond to well-defined compact structures formed by cubes and four-member rings made of water's hydrogen bonds interacting with a negative kernel formed by O2- with five water molecules, O2-(H2O)5, in which the negative charge is localized in the first four water molecules, while the fifth molecule provides geometrical stability. We assess the clusters' energetic stability based on dissociation energies, analyze electron detachment energies to understand its geometrical evolution, and investigate its charge distribution based upon isosurfaces of the highest occupied molecular orbital (HOMO). This research can help provide theoretical insight into the starting steps of nucleation of water clusters around ionic particles.
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Affiliation(s)
- N Gregory
- Maggie L. Walker Governor's School , Richmond , Virginia 23220 , United States
| | - J U Reveles
- Advanced Career Education Center at Highland Springs , Highland Springs , Virginia 23075 , United States
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14
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Abstract
Abstract
Hydrogen-bond (HB) patterns correspond to topologically distinct isomers of water clusters, and can be expressed by digraphs. The HB pattern is used to divide the configuration space of water cluster at a finite temperature. The populations of the HB patterns are transformed into the relative Helmholtz energies. The method is based on the combination of molecular simulation with graph theory. At a finite temperature it can be observed that other isomers than local minimum structures on the potential energy surface are highly populated. The dipole moment of a constituent molecule in a water cluster is enhanced depending on the local HB network around the water molecule. Rooted digraph is used to represent topologically distinct isomers of protonated water (PW) clusters. O–H bonds of PW clusters are classified into 10 topological types based on the combination of the local HB types of the contributing water molecules to the O–H bond. If the topological type is the same, vibrational frequencies of those O–H bonds of PW clusters are similar even in different isomers; i.e. vibrational frequency of O–H bond is transferable, and can be used as a vibrational spectral signature of PW clusters.
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Affiliation(s)
- Misako Aida
- Department of Chemistry, Graduate School of Science, Hiroshima University , Higashi-Hiroshima , Japan
- Center for Quantum Life Sciences, Hiroshima University , Higashi-Hiroshima , Japan
| | - Dai Akase
- Department of Chemistry, Graduate School of Science, Hiroshima University , Higashi-Hiroshima , Japan
- Center for Quantum Life Sciences, Hiroshima University , Higashi-Hiroshima , Japan
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15
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Miao J, Nie Y, Xiong Z, Chai Y, Fu S, Yan H. Stimulus-responsive reversible thermochromism and exciplex emission of a Zn(ii) complex and selective sensing of NH3 gas. Dalton Trans 2019; 48:5000-5006. [DOI: 10.1039/c9dt00764d] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A Zn(ii) complex exhibits reversible thermochromism and emission switch, and the resulting free radical species responds fast and selectively toward NH3.
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Affiliation(s)
- Jinling Miao
- School of Chemistry and Chemical Engineering
- Institute for Smart Materials & Engineering
- University of Jinan
- 250022 Jinan
- P. R. China
| | - Yong Nie
- School of Chemistry and Chemical Engineering
- Institute for Smart Materials & Engineering
- University of Jinan
- 250022 Jinan
- P. R. China
| | - Zhixin Xiong
- School of Chemistry and Chemical Engineering
- Institute for Smart Materials & Engineering
- University of Jinan
- 250022 Jinan
- P. R. China
| | - Yongshuai Chai
- School of Chemistry and Chemical Engineering
- Institute for Smart Materials & Engineering
- University of Jinan
- 250022 Jinan
- P. R. China
| | - Shuqing Fu
- School of Chemistry and Chemical Engineering
- Institute for Smart Materials & Engineering
- University of Jinan
- 250022 Jinan
- P. R. China
| | - Hong Yan
- State Key Laboratory of Coordination Chemistry
- School of Chemistry and Chemical Engineering
- Nanjing University
- 210023 Nanjing
- P. R. China
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16
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Ünal A, Bozkaya U. Anionic water pentamer and hexamer clusters: An extensive study of structures and energetics. J Chem Phys 2018; 148:124307. [DOI: 10.1063/1.5025233] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Aslı Ünal
- Department of Chemistry, Hacettepe University, Ankara 06800, Turkey
| | - Uğur Bozkaya
- Department of Chemistry, Hacettepe University, Ankara 06800, Turkey
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17
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Temelso B, Klein KL, Mabey JW, Pérez C, Pate BH, Kisiel Z, Shields GC. Exploring the Rich Potential Energy Surface of (H2O)11 and Its Physical Implications. J Chem Theory Comput 2018; 14:1141-1153. [DOI: 10.1021/acs.jctc.7b00938] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Berhane Temelso
- Provost’s
Office and Department of Chemistry, Furman University, Greenville, South Carolina 29613, United States
- Dean’s
Office, College of Arts and Sciences, and Department of Chemistry, Bucknell University, Lewisburg, Pennsylvania 17837, United States
| | - Katurah L. Klein
- Dean’s
Office, College of Arts and Sciences, and Department of Chemistry, Bucknell University, Lewisburg, Pennsylvania 17837, United States
| | - Joel W. Mabey
- Dean’s
Office, College of Arts and Sciences, and Department of Chemistry, Bucknell University, Lewisburg, Pennsylvania 17837, United States
| | - Cristóbal Pérez
- Department
of Chemistry, University of Virginia, McCormick Road, Charlottesville, Virginia 22904-4319, United States
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chausse 149, D-22761 Hamburg, Germany
| | - Brooks H. Pate
- Department
of Chemistry, University of Virginia, McCormick Road, Charlottesville, Virginia 22904-4319, United States
| | - Zbigniew Kisiel
- Institute
of Physics, Polish Academy of Sciences, Al. Lotników 32/46, 02-668 Warszawa, Poland
| | - George C. Shields
- Provost’s
Office and Department of Chemistry, Furman University, Greenville, South Carolina 29613, United States
- Dean’s
Office, College of Arts and Sciences, and Department of Chemistry, Bucknell University, Lewisburg, Pennsylvania 17837, United States
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18
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Wang B, Jiang W, Gao Y, Zhang Z, Sun C, Liu F, Wang Z. Energetics competition in centrally four-coordinated water clusters and Raman spectroscopic signature for hydrogen bonding. RSC Adv 2017. [DOI: 10.1039/c6ra28335g] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Viaseparating the H-bonded neighbour molecules of centrally four-coordinated water molecules from other molecules in outer cages, the calculations discover these two regions interact competitively with the central molecule.
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Affiliation(s)
- Bo Wang
- Institute of Atomic and Molecular Physics
- Jilin University
- Changchun 130012
- China
- Jilin Provincial Key Laboratory of Applied Atomic and Molecular Spectroscopy
| | - Wanrun Jiang
- Institute of Atomic and Molecular Physics
- Jilin University
- Changchun 130012
- China
- Jilin Provincial Key Laboratory of Applied Atomic and Molecular Spectroscopy
| | - Yang Gao
- Institute of Atomic and Molecular Physics
- Jilin University
- Changchun 130012
- China
- Jilin Provincial Key Laboratory of Applied Atomic and Molecular Spectroscopy
| | - Zhiyuan Zhang
- Institute of Atomic and Molecular Physics
- Jilin University
- Changchun 130012
- China
- Jilin Provincial Key Laboratory of Applied Atomic and Molecular Spectroscopy
| | - Changqing Sun
- School of Electrical and Electronic Engineering
- Nanyang Technological University
- Singapore 639798
- Singapore
| | - Fang Liu
- Institute of Atomic and Molecular Physics
- Jilin University
- Changchun 130012
- China
- Jilin Provincial Key Laboratory of Applied Atomic and Molecular Spectroscopy
| | - Zhigang Wang
- Institute of Atomic and Molecular Physics
- Jilin University
- Changchun 130012
- China
- Jilin Provincial Key Laboratory of Applied Atomic and Molecular Spectroscopy
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19
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20
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Reveles JU, Saoud KM, El-Shall MS. Water inhibits CO oxidation on gold cations in the gas phase. Structures and binding energies of the sequential addition of CO, H2O, O2, and N2 onto Au+. Phys Chem Chem Phys 2016; 18:28606-28616. [DOI: 10.1039/c6cp05431e] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
We report a detailed experimental and theoretical study of the gas phase reactivity of Au+ with CO, O2, N2 and their mixtures in the presence of a trace amount of water impurity.
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Affiliation(s)
| | - Khaled M. Saoud
- Liberal Arts and Sciences Program
- Virginia Commonwealth University in Qatar
- Qatar
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21
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Systematic testing of Gaussian and complete basis set methods with dispersion corrections for environmentally relevant clusters. Chem Phys Lett 2014. [DOI: 10.1016/j.cplett.2014.09.064] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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22
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Gil-García R, Gómez-Saiz P, Díez-Gómez V, Madariaga G, Insausti M, Lezama L, Cuevas JV, García-Tojal J. Thiosemicarbazonecopper(II) compounds with halide/hexafluorosilicate anions: Structure, water clusters, non-covalent interactions and magnetism. Polyhedron 2014. [DOI: 10.1016/j.poly.2014.07.032] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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23
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Zhu YP, Liu YR, Huang T, Jiang S, Xu KM, Wen H, Zhang WJ, Huang W. Theoretical Study of the Hydration of Atmospheric Nucleation Precursors with Acetic Acid. J Phys Chem A 2014; 118:7959-74. [DOI: 10.1021/jp506226z] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yu-Peng Zhu
- Laboratory of Atmospheric Physico-Chemistry, Anhui Institute of Optics & Fine Mechanics, Chinese Academy of Sciences, Hefei, Anhui 230031, China
| | - Yi-Rong Liu
- Laboratory of Atmospheric Physico-Chemistry, Anhui Institute of Optics & Fine Mechanics, Chinese Academy of Sciences, Hefei, Anhui 230031, China
| | - Teng Huang
- Laboratory of Atmospheric Physico-Chemistry, Anhui Institute of Optics & Fine Mechanics, Chinese Academy of Sciences, Hefei, Anhui 230031, China
| | - Shuai Jiang
- Laboratory of Atmospheric Physico-Chemistry, Anhui Institute of Optics & Fine Mechanics, Chinese Academy of Sciences, Hefei, Anhui 230031, China
| | - Kang-Ming Xu
- Laboratory of Atmospheric Physico-Chemistry, Anhui Institute of Optics & Fine Mechanics, Chinese Academy of Sciences, Hefei, Anhui 230031, China
| | - Hui Wen
- Laboratory of Atmospheric Physico-Chemistry, Anhui Institute of Optics & Fine Mechanics, Chinese Academy of Sciences, Hefei, Anhui 230031, China
| | - Wei-Jun Zhang
- Laboratory of Atmospheric Physico-Chemistry, Anhui Institute of Optics & Fine Mechanics, Chinese Academy of Sciences, Hefei, Anhui 230031, China
- School of Environmental Science & Optoelectronic Technology, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Wei Huang
- Laboratory of Atmospheric Physico-Chemistry, Anhui Institute of Optics & Fine Mechanics, Chinese Academy of Sciences, Hefei, Anhui 230031, China
- School of Environmental Science & Optoelectronic Technology, University of Science and Technology of China, Hefei, Anhui 230026, China
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24
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Akase D, Aida M. Distribution of topologically distinct isomers of water clusters and dipole moments of constituent water molecules at finite atmospheric temperatures. J Phys Chem A 2014; 118:7911-24. [PMID: 25111018 DOI: 10.1021/jp504854f] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Hydrogen-bonding (HB) patterns correspond to topologically distinct isomers of a water cluster and can be expressed by digraphs. We make use of the HB pattern to divide the configuration space of a water cluster ((H2O)n, n = 3-8) at a finite temperature. Each configuration of a water cluster generated in Monte Carlo (MC) simulation is classified into an HB pattern. The number of observed HB patterns increases exponentially with the cluster size, whereas the population of the most abundant HB pattern decreases. The populations of the HB patterns are transformed into the relative Helmholtz energies. At a finite temperature, it can be observed that isomers other than local minimum structures on the potential energy surface are highly populated. The dipole moment of a constituent molecule in a water cluster is enhanced, depending on the molecular circumstance. The change is rationalized by the difference in the local HB type of the water molecule in the HB network.
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Affiliation(s)
- Dai Akase
- Center for Quantum Life Sciences, and Department of Chemistry, Graduate School of Science, Hiroshima University , 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8526, Japan
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25
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Hao J, Li S, Jiang X, Huang C, Wang C. Rapid evaluation of individual hydrogen bonding energies in linear water chains. Chem Res Chin Univ 2014. [DOI: 10.1007/s40242-014-4047-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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26
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Temelso B, Alser KA, Gauthier A, Palmer AK, Shields GC. Structural Analysis of α-Fetoprotein (AFP)-like Peptides with Anti-Breast-Cancer Properties. J Phys Chem B 2014; 118:4514-26. [DOI: 10.1021/jp500017b] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Berhane Temelso
- Dean’s
Office, College of Arts and Sciences, and Department of Chemistry, Bucknell University, Lewisburg, Pennsylvania 17837, United States
- Dean’s Office, College of Science and Technology, and Department of Chemistry & Physics, Armstrong Atlantic State University, 11935 Abercorn Street, Savannah, Georgia 31419, United States
| | - Katherine A. Alser
- Dean’s
Office, College of Arts and Sciences, and Department of Chemistry, Bucknell University, Lewisburg, Pennsylvania 17837, United States
| | - Arianne Gauthier
- Dean’s Office, College of Science and Technology, and Department of Chemistry & Physics, Armstrong Atlantic State University, 11935 Abercorn Street, Savannah, Georgia 31419, United States
| | - Amber Kay Palmer
- Dean’s Office, College of Science and Technology, and Department of Chemistry & Physics, Armstrong Atlantic State University, 11935 Abercorn Street, Savannah, Georgia 31419, United States
| | - George C. Shields
- Dean’s
Office, College of Arts and Sciences, and Department of Chemistry, Bucknell University, Lewisburg, Pennsylvania 17837, United States
- Dean’s Office, College of Science and Technology, and Department of Chemistry & Physics, Armstrong Atlantic State University, 11935 Abercorn Street, Savannah, Georgia 31419, United States
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27
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Liu YR, Wen H, Huang T, Lin XX, Gai YB, Hu CJ, Zhang WJ, Huang W. Structural Exploration of Water, Nitrate/Water, and Oxalate/Water Clusters with Basin-Hopping Method Using a Compressed Sampling Technique. J Phys Chem A 2014; 118:508-16. [DOI: 10.1021/jp4109128] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yi-Rong Liu
- Laboratory of Atmospheric Physico-Chemistry, Anhui Institute of Optics & Fine Mechanics, Chinese Academy of Sciences, 350 Shushan Lake Road, Hefei, Anhui 230031, China
| | - Hui Wen
- Laboratory of Atmospheric Physico-Chemistry, Anhui Institute of Optics & Fine Mechanics, Chinese Academy of Sciences, 350 Shushan Lake Road, Hefei, Anhui 230031, China
| | - Teng Huang
- Laboratory of Atmospheric Physico-Chemistry, Anhui Institute of Optics & Fine Mechanics, Chinese Academy of Sciences, 350 Shushan Lake Road, Hefei, Anhui 230031, China
| | - Xiao-Xiao Lin
- Laboratory of Atmospheric Physico-Chemistry, Anhui Institute of Optics & Fine Mechanics, Chinese Academy of Sciences, 350 Shushan Lake Road, Hefei, Anhui 230031, China
| | - Yan-Bo Gai
- Laboratory of Atmospheric Physico-Chemistry, Anhui Institute of Optics & Fine Mechanics, Chinese Academy of Sciences, 350 Shushan Lake Road, Hefei, Anhui 230031, China
| | - Chang-Jin Hu
- Laboratory of Atmospheric Physico-Chemistry, Anhui Institute of Optics & Fine Mechanics, Chinese Academy of Sciences, 350 Shushan Lake Road, Hefei, Anhui 230031, China
| | - Wei-Jun Zhang
- Laboratory of Atmospheric Physico-Chemistry, Anhui Institute of Optics & Fine Mechanics, Chinese Academy of Sciences, 350 Shushan Lake Road, Hefei, Anhui 230031, China
- School of Environmental Science & Optoelectronic Technology, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China
| | - Wei Huang
- Laboratory of Atmospheric Physico-Chemistry, Anhui Institute of Optics & Fine Mechanics, Chinese Academy of Sciences, 350 Shushan Lake Road, Hefei, Anhui 230031, China
- School of Environmental Science & Optoelectronic Technology, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China
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28
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Structure and thermodynamics of H3O+(H2O)8 clusters: A combined molecular dynamics and quantum mechanics approach. COMPUT THEOR CHEM 2013. [DOI: 10.1016/j.comptc.2013.07.039] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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29
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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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30
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Howard JC, Tschumper GS. Wavefunction methods for the accurate characterization of water clusters. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2013. [DOI: 10.1002/wcms.1168] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
| | - Gregory S. Tschumper
- Department of Chemistry and Biochemistry University of Mississippi, University Mississippi USA
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31
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León I, Millán J, Cocinero EJ, Lesarri A, Fernández JA. Magic Numbers in the Solvation of the Propofol Dimer. Chemphyschem 2013; 14:1558-62. [DOI: 10.1002/cphc.201300205] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Indexed: 11/09/2022]
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32
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Liu GL, Li H. Auxiliary ligand-controlled supramolecular assembly of three Cd(ii) coordination polymers based on a (E)-3-(quinolin-4-yl) acrylic acid: syntheses, structures and photoluminescent properties. CrystEngComm 2013. [DOI: 10.1039/c3ce40864g] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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33
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Wang QQ, Day VW, Bowman-James K. Chemistry and Structure of a Host–Guest Relationship: The Power of NMR and X-ray Diffraction in Tandem. J Am Chem Soc 2012. [DOI: 10.1021/ja3096762] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Qi-Qiang Wang
- Department
of Chemistry, University of Kansas, Lawrence, Kansas 66045, United States
| | - Victor W. Day
- Department
of Chemistry, University of Kansas, Lawrence, Kansas 66045, United States
| | - Kristin Bowman-James
- Department
of Chemistry, University of Kansas, Lawrence, Kansas 66045, United States
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34
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ELLABAAN MOSTAFAMH, ONG YEWSOON, NGUYEN QC, KUO JERLAI. EVOLUTIONARY DISCOVERY OF TRANSITION STATES IN WATER CLUSTERS. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2012. [DOI: 10.1142/s0219633612500654] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
As a basic Aristotle element, water is the most abundant and more importantly crucial substance on earth. Without water, there would not be any form of life as we know. Understanding many phenomena in water such as water evaporation and ice melting and formation requires a deep understanding of hydrogen bond breaking and formation. In particular transition states play a key role in the understanding of such hydrogen bond behavior. Transition states, unlike other metastable states, are energy maxima along the minimum energy path connecting two isomers of molecular clusters. Geometry optimization of transition state structures, however, is a difficult task, and becomes even more arduous, especially when dealing with complex biochemical systems using first-principles calculations. In this paper, a novel molecular memetic algorithm (MOL-MA) composing of specially designed molecular-based water evolutionary operators coupled with a transition-state-local search solver and valley adaptive clearing scheme for the discovery of multiple precise transition states structures is proposed. The transition states of water clusters up to four water molecules uncovered using MOL-MA are reported. MOL-MA is shown not only to reproduce previously found transition states in water clusters, but also established newly discovered transition states for sizes 2–4 water molecules. The search performance of MOL-MA is also shown to outperform its compeers when pitted against those reported in the literature for finding transition states as well as recent advances in niching algorithms in terms of solution precision, computational effort, and number of transition states uncovered.
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Affiliation(s)
- MOSTAFA M. H. ELLABAAN
- Center of Computational Intelligence, School of Computer Engineering, Nanyang Technological University, Singapore
| | - YEW SOON ONG
- Center of Computational Intelligence, School of Computer Engineering, Nanyang Technological University, Singapore
| | - Q. C. NGUYEN
- Singapore Institute of Manufacturing Technology, A*Star, Singapore
| | - JER-LAI KUO
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, Taiwan
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35
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Temelso B, Phan TN, Shields GC. Computational Study of the Hydration of Sulfuric Acid Dimers: Implications for Acid Dissociation and Aerosol Formation. J Phys Chem A 2012; 116:9745-58. [DOI: 10.1021/jp3054394] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Berhane Temelso
- Dean’s Office, College of Arts and Sciences,
and Department of Chemistry, Bucknell University, Lewisburg, Pennsylvania 17837,
United States
| | - Thuong Ngoc Phan
- Dean’s Office, College of Arts and Sciences,
and Department of Chemistry, Bucknell University, Lewisburg, Pennsylvania 17837,
United States
| | - George C. Shields
- Dean’s Office, College of Arts and Sciences,
and Department of Chemistry, Bucknell University, Lewisburg, Pennsylvania 17837,
United States
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36
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Husar DE, Temelso B, Ashworth AL, Shields GC. Hydration of the Bisulfate Ion: Atmospheric Implications. J Phys Chem A 2012; 116:5151-63. [DOI: 10.1021/jp300717j] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Devon E. Husar
- Dean’s Office, College of
Arts and Sciences,
and Department of Chemistry, Bucknell University, Lewisburg, Pennsylvania 17837, United States
| | - Berhane Temelso
- Dean’s Office, College of
Arts and Sciences,
and Department of Chemistry, Bucknell University, Lewisburg, Pennsylvania 17837, United States
| | - Alexa L. Ashworth
- Dean’s Office, College of
Arts and Sciences,
and Department of Chemistry, Bucknell University, Lewisburg, Pennsylvania 17837, United States
| | - George C. Shields
- Dean’s Office, College of
Arts and Sciences,
and Department of Chemistry, Bucknell University, Lewisburg, Pennsylvania 17837, United States
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37
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Temelso B, Morrell TE, Shields RM, Allodi MA, Wood EK, Kirschner KN, Castonguay TC, Archer KA, Shields GC. Quantum Mechanical Study of Sulfuric Acid Hydration: Atmospheric Implications. J Phys Chem A 2012; 116:2209-24. [DOI: 10.1021/jp2119026] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Berhane Temelso
- Dean’s Office, College
of Arts and Sciences, and Department of Chemistry, Bucknell University, Lewisburg, Pennsylvania
17837, United States
| | - Thomas E. Morrell
- Dean’s Office, College
of Arts and Sciences, and Department of Chemistry, Bucknell University, Lewisburg, Pennsylvania
17837, United States
| | - Robert M. Shields
- Dean’s Office, College
of Arts and Sciences, and Department of Chemistry, Bucknell University, Lewisburg, Pennsylvania
17837, United States
| | - Marco A. Allodi
- Dean’s Office, College
of Arts and Sciences, and Department of Chemistry, Bucknell University, Lewisburg, Pennsylvania
17837, United States
| | - Elena K. Wood
- Dean’s Office, College
of Arts and Sciences, and Department of Chemistry, Bucknell University, Lewisburg, Pennsylvania
17837, United States
| | - Karl N. Kirschner
- Department of Simulation
Engineering, Fraunhofer-Institute for Algorithms and Scientific Computing (SCAI), Schloss Birlinghoven,
53754 Sankt Augustin, Germany
| | - Thomas C. Castonguay
- Department of Chemistry, Iona College, New Rochelle, New York
10801, United States
| | - Kaye A. Archer
- Dean’s Office, College
of Arts and Sciences, and Department of Chemistry, Bucknell University, Lewisburg, Pennsylvania
17837, United States
| | - George C. Shields
- Dean’s Office, College
of Arts and Sciences, and Department of Chemistry, Bucknell University, Lewisburg, Pennsylvania
17837, United States
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38
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Hossain MA, Işıklan M, Pramanik A, Saeed MA, Fronczek FR. Anion Cluster: Assembly of Dihydrogen Phosphates for the Formation of a Cyclic Anion Octamer. CRYSTAL GROWTH & DESIGN 2012; 12:567-571. [PMID: 22435043 PMCID: PMC3306550 DOI: 10.1021/cg201464k] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Structural characterization of a dihydrogen phosphate complex of triprotonated tris[2-(2-thienylmethylamino)ethyl] amine shows that eight dihydrogen phosphate anions are assembled around the host by strong interactions of H-bond donors and acceptors to form a new type of cyclic anion octamer as (H(2)PO(4) (-))(8), an analogy of cyclic water octamer. The presence of an anion cluster has also been identified by electrospray ionization mass spectrometry and (31)P NMR experiments.
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Affiliation(s)
- Md. Alamgir Hossain
- Department of Chemistry and Biochemistry, Jackson State University, Jackson, Mississippi 39217, United States
| | - Muhammet Işıklan
- Department of Chemistry and Biochemistry, Jackson State University, Jackson, Mississippi 39217, United States
| | - Avijit Pramanik
- Department of Chemistry and Biochemistry, Jackson State University, Jackson, Mississippi 39217, United States
| | - Musabbir A. Saeed
- Department of Chemistry and Biochemistry, Jackson State University, Jackson, Mississippi 39217, United States
| | - Frank R. Fronczek
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
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39
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Wang QQ, Day VW, Bowman-James K. Supramolecular Encapsulation of Tetrahedrally Hydrated Guests in a Tetrahedron Host. Angew Chem Int Ed Engl 2012; 51:2119-23. [DOI: 10.1002/anie.201106090] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2011] [Revised: 11/28/2011] [Indexed: 11/12/2022]
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40
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Wang QQ, Day VW, Bowman-James K. Supramolecular Encapsulation of Tetrahedrally Hydrated Guests in a Tetrahedron Host. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201106090] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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41
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Li T, Huang XH, Zhao YF, Li HH, Wu ST, Huang CC. An unusual double T5(2) water tape trapped in silver(i) coordination polymer hosts: influence of the solvent on the assembly of Ag(i)-4,4′-bipyridine chains with trans-cyclohexanedicarboxylate and their luminescent properties. Dalton Trans 2012; 41:12872-81. [DOI: 10.1039/c2dt31847d] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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42
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Saeed MA, Pramanik A, Wong BM, Haque SA, Powell DR, Chand DK, Hossain MA. Self-assembly of ordered water tetramers in an encapsulated [Br(H2O)12]− complex. Chem Commun (Camb) 2012; 48:8631-3. [DOI: 10.1039/c2cc30767g] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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43
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Chakraborty B, Paine TK. Synthesis and characterization of cobalt(II)–salicylate complexes derived from N4-donor ligands: Stabilization of a hexameric water cluster in the lattice host of a cobalt(III)–salicylate complex. Inorganica Chim Acta 2011. [DOI: 10.1016/j.ica.2011.09.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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44
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Temelso B, Archer KA, Shields GC. Benchmark Structures and Binding Energies of Small Water Clusters with Anharmonicity Corrections. J Phys Chem A 2011; 115:12034-46. [DOI: 10.1021/jp2069489] [Citation(s) in RCA: 256] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Berhane Temelso
- Dean’s Office, College of Arts and Sciences, and Department of Chemistry, Bucknell University, Lewisburg, Pennsylvania 17837, United States
| | - Kaye A. Archer
- Dean’s Office, College of Arts and Sciences, and Department of Chemistry, Bucknell University, Lewisburg, Pennsylvania 17837, United States
| | - George C. Shields
- Dean’s Office, College of Arts and Sciences, and Department of Chemistry, Bucknell University, Lewisburg, Pennsylvania 17837, United States
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What is the best density functional to describe water clusters: evaluation of widely used density functionals with various basis sets for (H2O) n (n = 1–10). Theor Chem Acc 2011. [DOI: 10.1007/s00214-011-0989-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Shields RM, Temelso B, Archer KA, Morrell TE, Shields GC. Accurate predictions of water cluster formation, (H₂O)(n=2-10). J Phys Chem A 2011; 114:11725-37. [PMID: 20882961 DOI: 10.1021/jp104865w] [Citation(s) in RCA: 161] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
An efficient mixed molecular dynamics/quantum mechanics model has been applied to the water cluster system. The use of the MP2 method and correlation consistent basis sets, with appropriate correction for BSSE, allows for the accurate calculation of electronic and free energies for the formation of clusters of 2-10 water molecules. This approach reveals new low energy conformers for (H(2)O)(n=7,9,10). The water heptamer conformers comprise five different structural motifs ranging from a three-dimensional prism to a quasi-planar book structure. A prism-like structure is favored energetically at low temperatures, but a chair-like structure is the global Gibbs free energy minimum past 200 K. The water nonamers exhibit less complexity with all the low energy structures shaped like a prism. The decamer has 30 conformers that are within 2 kcal/mol of the Gibbs free energy minimum structure at 298 K. These structures are categorized into four conformer classes, and a pentagonal prism is the most stable structure from 0 to 320 K. Results can be used as benchmark values for empirical water models and density functionals, and the method can be applied to larger water clusters.
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Affiliation(s)
- Robert M Shields
- Dean's Office, College of Arts and Sciences, and Department of Chemistry, Bucknell University, Lewisburg, Pennsylvania 17837, USA
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Sun D, Wei ZH, Yang CF, Wang DF, Zhang N, Huang RB, Zheng LS. pH-Dependent Ag(i) coordination architectures constructed from 4-cyanopyridine and phthalic acid: from discrete structure to 2D sheet. CrystEngComm 2011. [DOI: 10.1039/c0ce00539h] [Citation(s) in RCA: 131] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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Steudel R, Steudel Y. Reversal of the relative stability of the isomeric radicals HSO and HOS upon hydration and their reactions with ozone. J Phys Chem A 2010; 114:4437-45. [PMID: 20218592 DOI: 10.1021/jp912012g] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The radical HSO is an oxidation product of pollutants such as H(2)S and CH(3)SH in Earth's atmosphere. For the first time, the interaction of HSO and its tautomer HOS with single water molecules to yield the hydrates HSO.nH(2)O and HOS.nH(2)O was studied for n = 1-3, applying the high-level G3X(MP2) theory. A large number of structures corresponding to local minima on the potential energy surfaces has been identified. While gaseous HSO is more stable than HOS, the enthalpy diffference between HSO.nH(2)O and HOS.nH(2)O decreases with increasing degree of hydration and becomes practically zero for n = 3. Thus, in aqueous solution as well as in fog and rain droplets, HOS is expected to compete with HSO. The barrier for the tautomerization of HSO to HOS is dramatically lowered by the presence of water molecules since a cyclic transition state allows a concerted proton shift within the system of neighboring hydrogen bonds. The corresponding activation enthalpy of only 73.5 kJ mol(-1) predicted for the transformation of HSO.2H(2)O into HOS.2H(2)O may be compared to the 202 kJ mol(-1) reported for the tautomerization of the unhydrated gaseous HSO/HOS molecules. The impact of water of hydration on the fundamental vibrational modes of HSO and HOS has also been studied. Furthermore, HOS is predicted to dimerize at low temperatures to give two van der Waals molecules with singlet (symmetry C(2)) or triplet configuration (symmetry C(2h)), the latter being more stable than the singlet isomer. The disproportionation of 2HSO to H(2)S and SO(2) is predicted to be exothermic by -263.5 kJ mol(-1). The reaction of HSO with ozone to HSO(2) and O(2) is also strongly exothermic by -274.0 kJ mol(-1) and seems to proceed without any barrier. HOS forms a 1:1 van der Waals complex with O(3); the redox reaction of its two components is calculated as exothermic by -410.9 kJ mol(-1) and results in a rather stable adduct between HOSO and O(2) with the structure of a peroxo isomer of HOSO(3). This unprecedented hydrogen peroxosulfite radical might open a novel route to atmospheric sulfate without the intermediate formation of SO(2) and SO(3).
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Affiliation(s)
- Ralf Steudel
- Institut für Chemie, Sekr. C2, Technische Universität Berlin, D-10623 Berlin, Germany
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Kang D, Dai J, Hou Y, Yuan J. Structure and vibrational spectra of small water clusters from first principles simulations. J Chem Phys 2010; 133:014302. [DOI: 10.1063/1.3462278] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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