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Michalczyk M, Kizior B, Zierkiewicz W, Scheiner S. Factors contributing to halogen bond strength and stretch or contraction of internal covalent bond. Phys Chem Chem Phys 2023; 25:2907-2915. [PMID: 36636920 DOI: 10.1039/d2cp05598h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The halogen bond formed by a series of Lewis acids TF3X (T = C, Si, Ge, Sn, Pb; X = Cl, Br, I) with NH3 is studied by quantum chemical calculations. The interaction energy is closely mimicked by the depth of the σ-hole on the X atom as well as the full electrostatic energy. There is a first trend by which the hole is deepened if the T atom to which X is attached becomes more electron-withdrawing: C > Si > Ge > Sn > Pb. On the other hand, larger more polarizable T atoms are better able to transmit the electron-withdrawing power of the F substituents. The combination of these two opposing factors leaves PbF3X forming the strongest XBs, followed by CF3X, with SiF3X engaging in the weakest bonds. The charge transfer from the NH3 lone pair into the σ*(TX) antibonding orbital tends to elongate the covalent TX bond, and this force is largest for the heavier X and T atoms. On the other hand, the contraction of this bond deepens the σ-hole at the X atom, which would enhance both the electrostatic component and the full interaction energy. This bond-shortening effect is greatest for the lighter X atoms. The combination of these two opposing forces leaves the T-X bond contracting for X = Cl and Br, but lengthening for I.
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Affiliation(s)
- Mariusz Michalczyk
- Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370, Wrocław, Poland.
| | - Beata Kizior
- Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370, Wrocław, Poland.
| | - Wiktor Zierkiewicz
- Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370, Wrocław, Poland.
| | - Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University Logan, Utah, 84322-0300, USA.
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2
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Benassi E, Vaganova T, Malykhin E, Gatilov Y, Nurtay L, Fan H. Intermolecular interactions in the crystalline structure of some polyhalogenated Di- And triamino Pyridines: Spectroscopical perspectives. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 281:121632. [PMID: 35868054 DOI: 10.1016/j.saa.2022.121632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 07/01/2022] [Accepted: 07/12/2022] [Indexed: 06/15/2023]
Abstract
Supramolecular synthon is identified as a unit and provides important structural and energetic information in the study of organic crystals. However, the direct estimation of the supramolecular interaction remains challenging. In the present work six polyhalogenated di- or triamino pyridines were synthesised, their crystalline structure was characterised, and corresponding supramolecular synthons were studied using a combination of quantum mechanical calculations and FT-IR and Raman spectroscopy. Some distinctive features were identified especially for three vibrational normal modes (RNMs) related to the pyridine ring (viz. RNM1, RNM3 and RNM7) in the vibrational spectra (FT-IR and Raman) of the solid samples, which are due to the supramolecular interactions, hydrogen bond (hb) in particular, according to the quantum mechanical calculations. The comparison between the IR and Raman spectra of experimental and simulated results indicates that the adjacent intermolecular hydrogen bonds between two same molecules extensively exist in the solid samples. Moreover, some quantitative correlation was established among the dimerisation energies for hb dimers (hb1 dimers for compounds 1 and 2), the ring structure defined by the distribution of the substituents and quantitative characteristics of the vibrational spectra, for instance, the splitting magnitudes for RNM3(2) in IR spectra and the peak gap between RNM1 and RNM2 in Raman spectra.
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Affiliation(s)
- Enrico Benassi
- Novosibirsk State University, Pirogova ul. 2, Novosibirsk, 630090, Russia.
| | - Tamara Vaganova
- Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Lavrentyev Prospekt 9, Novosibirsk, 630090, Russia
| | - Evgenij Malykhin
- Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Lavrentyev Prospekt 9, Novosibirsk, 630090, Russia
| | - Yurij Gatilov
- Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Lavrentyev Prospekt 9, Novosibirsk, 630090, Russia
| | - Lazzat Nurtay
- Department of Chemistry, School of Sciences and Humanities, Nazarbayev University, Qabanbay Batyr 53, Nursultan, 010000, Kazakhstan
| | - Haiyan Fan
- Department of Chemistry, School of Sciences and Humanities, Nazarbayev University, Qabanbay Batyr 53, Nursultan, 010000, Kazakhstan
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3
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Feng W, Li D, Cheng L. Theoretical study on L-H +-L with identical donors: short strong hydrogen bond or not? J Chem Phys 2022; 157:094302. [DOI: 10.1063/5.0103228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Short strong hydrogen bonds (SSHBs) play crucial role in many chemical processes. Recently, as the representative of SSHBs, [F-H-F]- was experimentally observed. [F-H-F]- has a symmetric structure, which can be described as a H+ acid shared by two terminal F- donors (F--H+-F-). To explore whether two identical donors are bound to result in SSHBs, we performed theoretical studies on a series of compounds (L-H+-L) with two identical electron donors (L corresponds to donors containing group 14, 15, 16 and 17 elements). The results show that identical donors do not definitely lead to SSHBs. Instead, typical hydrogen bonds also exist. We found that both electronegativity and basicity contribute to the patterns of hydrogen bonds, where more electronegative and weaker donors benefit to SSHBs. Besides, it was found that zero-point energies also respond to the hydrogen bonding systems. This systemic work is expected to provide more insights into SSHBs.
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Affiliation(s)
- Wanwan Feng
- Anhui University Department of Chemistry, China
| | - Dan Li
- Anhui University - Qingyuan Campus, China
| | - Longjiu Cheng
- Department of Chemistry, Anhui University College of Chemistry and Chemical Engineering, China
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4
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Theoretical investigation on the improper hydrogen bond in κ-carrabiose⋯Y (Y = HF, HCl, HBr, NH 3, H 2O, and H 2S) complexes. J Mol Model 2021; 27:292. [PMID: 34546413 DOI: 10.1007/s00894-021-04904-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 09/07/2021] [Indexed: 10/20/2022]
Abstract
The nature of H-bonds in κ-carrabiose⋯Y (Y = HF, HCl, HBr, NH3, H2O, and H2S) complexes was studied. For this aim, the structure of isolated κ-carrabiose was optimized using three global hybrids functional: B3LYP, PBE0, and M06-2X combined with 6-311G** basis set. Subsequently, the κ-carrabiose in the presence of HF, HCl, HBr, NH3, H2O, and H2S was optimized using the CBS-4 M method. NBO analyses were then carried out at the MP2/6-311G** level of theory. A particular interest was focused on C(18)-H(34)⋯Y bond. The results reveal that the C(18)-H(34)⋯Y bond is an improper H-bond since a significant contraction of C(18)-H(34) was observed during the complexation leading to a significant blueshifted stretching frequency. The NBO analyses have shown that the formation of the improper H-bonds C(18)-H(34)⋯Y (Y = F, Cl, Br, N, O, and S) is principally due to the increase of the s-character of the hybrid orbital in carbon atom (rehybridization) in κ-carrabiose⋯Y complexes. Regarding the polarization, it was proved that more the H-bond center (carbon in C(18)-H(34)⋯Y) becomes less positive, the hydrogen more positive, and Y more negative; more the contraction of the C(18)-H(34) bond is important. It was also confirmed for intramolecular H-bonds in κ-carrabiose⋯Y complexes that the rehybridization is responsible for H-bonds nature either proper or improper.
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Gupta AK, Gamoke BC, Raghavachari K. Interaction-Deletion: A Composite Energy Method for the Optimization of Molecular Systems Selectively Removing Specific Nonbonded Interactions. J Phys Chem A 2021; 125:4668-4682. [PMID: 34014684 DOI: 10.1021/acs.jpca.1c02918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The complex interactions between different portions of a large molecule can be challenging to analyze through traditional electronic structure calculations. Moreover, standard methods cannot easily quantify the physical consequences of individual pairwise interactions inside a molecule. By creating a set of molecular fragments, we propose a composite energy method to explore changes in a molecule caused by removing selected nonbonded interactions between different molecular portions. Energies and forces are easily obtained with this composite approach, allowing geometry optimizations that lead to chemically meaningful structures that describe how the omitted interactions contribute to changes in the local geometrical minima. We illustrate the application of our new hybrid scheme by computing the influence of intramolecular hydrogen-bonding interactions in two small molecules: 1,6-(tG+G+TG+G+g-)-hexanediol and a cyclic analogue, cis-1,4-cyclohexanediol. The resulting structural and energetic changes are interpreted to yield key physical insights and quantify concepts such as "preparation energy" or "reorganization energy". We demonstrate that the composite method can be extended to larger molecular systems by showing its application on a Si(100) surface model containing interactions between dissociated ammonia molecules on adjacent surface dimers. The scheme's efficacy is also tested by applying it to systems having multiple intramolecular interactions, viz., 310-polyglycine and H+GPGG. Furthermore, the cooperative nature of intramolecular hydrogen bonds is explored by using interaction-deletion in 2-nitrobenzene-1,3-diol.
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Affiliation(s)
- Ankur K Gupta
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Benjamin C Gamoke
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Krishnan Raghavachari
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
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6
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Lu J, Scheiner S. Relationships between Bond Strength and Spectroscopic Quantities in H-Bonds and Related Halogen, Chalcogen, and Pnicogen Bonds. J Phys Chem A 2020; 124:7716-7725. [DOI: 10.1021/acs.jpca.0c05936] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Jia Lu
- Department of Chemistry and Biochemistry, Utah State University , Logan, Utah 84322-0300, United States
| | - Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University , Logan, Utah 84322-0300, United States
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7
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Baiz CR, Błasiak B, Bredenbeck J, Cho M, Choi JH, Corcelli SA, Dijkstra AG, Feng CJ, Garrett-Roe S, Ge NH, Hanson-Heine MWD, Hirst JD, Jansen TLC, Kwac K, Kubarych KJ, Londergan CH, Maekawa H, Reppert M, Saito S, Roy S, Skinner JL, Stock G, Straub JE, Thielges MC, Tominaga K, Tokmakoff A, Torii H, Wang L, Webb LJ, Zanni MT. Vibrational Spectroscopic Map, Vibrational Spectroscopy, and Intermolecular Interaction. Chem Rev 2020; 120:7152-7218. [PMID: 32598850 PMCID: PMC7710120 DOI: 10.1021/acs.chemrev.9b00813] [Citation(s) in RCA: 171] [Impact Index Per Article: 42.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Vibrational spectroscopy is an essential tool in chemical analyses, biological assays, and studies of functional materials. Over the past decade, various coherent nonlinear vibrational spectroscopic techniques have been developed and enabled researchers to study time-correlations of the fluctuating frequencies that are directly related to solute-solvent dynamics, dynamical changes in molecular conformations and local electrostatic environments, chemical and biochemical reactions, protein structural dynamics and functions, characteristic processes of functional materials, and so on. In order to gain incisive and quantitative information on the local electrostatic environment, molecular conformation, protein structure and interprotein contacts, ligand binding kinetics, and electric and optical properties of functional materials, a variety of vibrational probes have been developed and site-specifically incorporated into molecular, biological, and material systems for time-resolved vibrational spectroscopic investigation. However, still, an all-encompassing theory that describes the vibrational solvatochromism, electrochromism, and dynamic fluctuation of vibrational frequencies has not been completely established mainly due to the intrinsic complexity of intermolecular interactions in condensed phases. In particular, the amount of data obtained from the linear and nonlinear vibrational spectroscopic experiments has been rapidly increasing, but the lack of a quantitative method to interpret these measurements has been one major obstacle in broadening the applications of these methods. Among various theoretical models, one of the most successful approaches is a semiempirical model generally referred to as the vibrational spectroscopic map that is based on a rigorous theory of intermolecular interactions. Recently, genetic algorithm, neural network, and machine learning approaches have been applied to the development of vibrational solvatochromism theory. In this review, we provide comprehensive descriptions of the theoretical foundation and various examples showing its extraordinary successes in the interpretations of experimental observations. In addition, a brief introduction to a newly created repository Web site (http://frequencymap.org) for vibrational spectroscopic maps is presented. We anticipate that a combination of the vibrational frequency map approach and state-of-the-art multidimensional vibrational spectroscopy will be one of the most fruitful ways to study the structure and dynamics of chemical, biological, and functional molecular systems in the future.
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Affiliation(s)
- Carlos R. Baiz
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, U.S.A
| | - Bartosz Błasiak
- Department of Physical and Quantum Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Jens Bredenbeck
- Johann Wolfgang Goethe-University, Institute of Biophysics, Max-von-Laue-Str. 1, 60438, Frankfurt am Main, Germany
| | - Minhaeng Cho
- Center for Molecular Spectroscopy and Dynamics, Seoul 02841, Republic of Korea
- Department of Chemistry, Korea University, Seoul 02841, Republic of Korea
| | - Jun-Ho Choi
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea
| | - Steven A. Corcelli
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, U.S.A
| | - Arend G. Dijkstra
- School of Chemistry and School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, U.K
| | - Chi-Jui Feng
- Department of Chemistry, James Franck Institute and Institute for Biophysical Dynamics, University of Chicago, Chicago, IL 60637, U.S.A
| | - Sean Garrett-Roe
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, U.S.A
| | - Nien-Hui Ge
- Department of Chemistry, University of California at Irvine, Irvine, CA 92697-2025, U.S.A
| | - Magnus W. D. Hanson-Heine
- School of Chemistry, University of Nottingham, Nottingham, University Park, Nottingham, NG7 2RD, U.K
| | - Jonathan D. Hirst
- School of Chemistry, University of Nottingham, Nottingham, University Park, Nottingham, NG7 2RD, U.K
| | - Thomas L. C. Jansen
- University of Groningen, Zernike Institute for Advanced Materials, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Kijeong Kwac
- Center for Molecular Spectroscopy and Dynamics, Seoul 02841, Republic of Korea
| | - Kevin J. Kubarych
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, MI 48109, U.S.A
| | - Casey H. Londergan
- Department of Chemistry, Haverford College, Haverford, Pennsylvania 19041, U.S.A
| | - Hiroaki Maekawa
- Department of Chemistry, University of California at Irvine, Irvine, CA 92697-2025, U.S.A
| | - Mike Reppert
- Chemical Physics Theory Group, Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Shinji Saito
- Department of Theoretical and Computational Molecular Science, Institute for Molecular Science, Myodaiji, Okazaki, 444-8585, Japan
| | - Santanu Roy
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6110, U.S.A
| | - James L. Skinner
- Institute for Molecular Engineering, University of Chicago, Chicago, IL 60637, U.S.A
| | - Gerhard Stock
- Biomolecular Dynamics, Institute of Physics, Albert Ludwigs University, 79104 Freiburg, Germany
| | - John E. Straub
- Department of Chemistry, Boston University, Boston, MA 02215, U.S.A
| | - Megan C. Thielges
- Department of Chemistry, Indiana University, 800 East Kirkwood, Bloomington, Indiana 47405, U.S.A
| | - Keisuke Tominaga
- Molecular Photoscience Research Center, Kobe University, Nada, Kobe 657-0013, Japan
| | - Andrei Tokmakoff
- Department of Chemistry, James Franck Institute and Institute for Biophysical Dynamics, University of Chicago, Chicago, IL 60637, U.S.A
| | - Hajime Torii
- Department of Applied Chemistry and Biochemical Engineering, Faculty of Engineering, and Department of Optoelectronics and Nanostructure Science, Graduate School of Science and Technology, Shizuoka University, 3-5-1 Johoku, Naka-Ku, Hamamatsu 432-8561, Japan
| | - Lu Wang
- Department of Chemistry and Chemical Biology, Institute for Quantitative Biomedicine, Rutgers University, 174 Frelinghuysen Road, Piscataway, NJ 08854, U.S.A
| | - Lauren J. Webb
- Department of Chemistry, The University of Texas at Austin, 105 E. 24th Street, STOP A5300, Austin, Texas 78712, U.S.A
| | - Martin T. Zanni
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706-1396, U.S.A
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8
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Oram BK, Bandyopadhyay B. Impact of donor acidity and acceptor anharmonicity on v c=o spectral shifts in O-H···O=C H-bonded ketone-alcohol complexes: An IR spectroscopic investigation. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 230:118070. [PMID: 31982658 DOI: 10.1016/j.saa.2020.118070] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 01/09/2020] [Accepted: 01/11/2020] [Indexed: 06/10/2023]
Abstract
O-H···O=C Hydrogen bonding (H-bonding) results in spectral shifts in both νO-H and νC=O modes. A large number of investigations exist in literature that focuses on how the spectral shifts vary with certain properties of the donors and acceptors. However information on how the magnitude of spectral shift is dictated individually by the donor and acceptor is not yet clear to us. Here, IR spectroscopy in room temperature CCl4 solution has been used to investigate how νC=O spectral shifts of ketones in H-bonded complexes with alcohols are influenced by change in donor and acceptor properties. For this purpose 25 number of O-H···O=C H-bonded complexes formed by 5 different ketones and 5 alcohols have been studied. The magnitude of red-shifts shown by the νC=O bands were found to show systematic trends with changing donor and acceptor species. It was found that for a particular ketone, the magnitude of shift increases monotonically with acidity of the alcohols. Spectral shifts were found to increase in a linear fashion with decreasing pKa of the donor alcohols. On the other hand, when the alcohol were kept fixed, the spectral shift was found to be dependent on the CO bond strength of the ketones. We found spectral shifts to linearly increase with increasing anharmonicity constant and decreasing dissociation energy of CO bond. Finally, it has been shown that there exist concomitant correlations of the spectral shifts with donor pKa and acceptor νC=O anharmonicity constant/bond dissociation energy. The relations have been validated for H-bonded complexes of 1,4-cyclohexanedione with the above mentioned five alcohols.
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Affiliation(s)
- Binod Kumar Oram
- Department of Chemistry, Malaviya National Institute of Technology Jaipur, Jaipur 302017, India
| | - Biman Bandyopadhyay
- Department of Chemistry, Malaviya National Institute of Technology Jaipur, Jaipur 302017, India.
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9
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Suvitha A, Venkataramanan NS, Sahara R, Kawazoe Y. A theoretical exploration of the intermolecular interactions between resveratrol and water: a DFT and AIM analysis. J Mol Model 2019; 25:56. [DOI: 10.1007/s00894-019-3941-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 01/24/2019] [Indexed: 12/27/2022]
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10
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A detailed theoretical and experimental study on the N H, P O and C O stretching frequencies in two new phosphoric triamides and a statistical comparison with analogous structures. Polyhedron 2019. [DOI: 10.1016/j.poly.2018.10.045] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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11
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Mayangsari TR, Park JM, Yusup LL, Gu J, Yoo JH, Kim HD, Lee WJ. Catalyzed Atomic Layer Deposition of Silicon Oxide at Ultralow Temperature Using Alkylamine. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:6660-6669. [PMID: 29768003 DOI: 10.1021/acs.langmuir.8b00147] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
We report the catalyzed atomic layer deposition (ALD) of silicon oxide using Si2Cl6, H2O, and various alkylamines. The density functional theory (DFT) calculations using the periodic slab model of the SiO2 surface were performed for the selection of alternative Lewis base catalysts with high catalytic activities. During the first half-reaction, the catalysts with less steric hindrance such as pyridine would be more effective than bulky alkylamines despite lower nucleophilicity. On the other hand, during the second half-reaction, the catalysts with a high nucleophilicity such as triethylamine (Et3N) would be more efficient because the steric hindrance is less critical. The in situ process monitoring shows that the calculated atomic charge is a good indicator for expecting the catalyst activity in the ALD reaction. The use of Et3N in the second half-reaction was essential to improving the growth rate as well as the step coverage of the film because the Et3N-catalyzed process deposited a SiO2 film with a step coverage of 98% that is better than 93% of the pyridine-catalyzed process. The adsorption of pyridine, ammonia (NH3), or trimethylamine (Me3N) salts was more favorable than that of Et3N, n-Pr3N, or iPr3N salts. Therefore, Et3N was expected to incorporate less amine salts in the film as compared to pyridine, and the compositional analyses confirmed that the concentrations of Cl and N by the Et3N-catalyzed process were significantly lower than those by the pyridine-catalyzed process.
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Affiliation(s)
- Tirta R Mayangsari
- Department of Nanotechnology and Advanced Material Engineering , Sejong University , Seoul 05006 , Republic of Korea
| | - Jae-Min Park
- Department of Nanotechnology and Advanced Material Engineering , Sejong University , Seoul 05006 , Republic of Korea
| | - Luchana L Yusup
- Department of Nanotechnology and Advanced Material Engineering , Sejong University , Seoul 05006 , Republic of Korea
| | - Jiyeon Gu
- Department of Nanotechnology and Advanced Material Engineering , Sejong University , Seoul 05006 , Republic of Korea
| | - Jin-Hyuk Yoo
- R&D Division , Jusung Engineering , Gwangju , Gyeonggi-do 12773 , Republic of Korea
| | - Heon-Do Kim
- R&D Division , Jusung Engineering , Gwangju , Gyeonggi-do 12773 , Republic of Korea
| | - Won-Jun Lee
- Department of Nanotechnology and Advanced Material Engineering , Sejong University , Seoul 05006 , Republic of Korea
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12
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McDowell SA. A computational study of hydrogen-bonded X3CH⋯YZ (X = Cl, F, NC; YZ = FLi, BF, CO, N2) complexes. Chem Phys Lett 2018. [DOI: 10.1016/j.cplett.2018.02.037] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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13
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Oliveira de Sousa DW, Nascimento MAC. Quantum Interference Contribution to the Dipole Moment of Diatomic Molecules. J Phys Chem A 2018; 122:1406-1412. [PMID: 29338264 DOI: 10.1021/acs.jpca.7b11760] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The interference energy partitioning analysis method developed by our group and used to study the nature of the chemical bond was extended to partition the electric dipole moment in quasi-classical and interference contributions. Our results show that interference participates in charge displacement in polar molecules, providing, directly or indirectly, a relevant contribution for the total dipole moment. A linear correlation was found between the interference contribution of the dipole moment from the bond electron group, μINT(bond), and the difference of electronegativity of the atoms which form the bond, ΔXAB. This interesting result reinforces the fact that electronegativity is not a property of an atom alone, but rather a property of the atom in the molecule and that ΔXAB can only be associated with that part of the total charge displacement resulting from the formation of the chemical bond. The partitioning of the total dipole moment into quasi-classical and interference contributions provides new insights about the reasons for the failure of the ΔXAB criterion in predicting the correct orientation of the dipole moment in several molecules. The results of the present work also bring additional evidence for the previously proposed mechanism of formation of polar bonds.
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14
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Yang F, Wu RZ, Yan CX, Yang X, Zhou DG, Zhou PP. Quantitative relationships between bond lengths, stretching vibrational frequencies, bond force constants, and bond orders in the hydrogen-bonded complexes involving hydrogen halides. Struct Chem 2017. [DOI: 10.1007/s11224-017-1048-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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15
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Chemistry is about energy and its changes: A critique of bond-length/bond-strength correlations. Coord Chem Rev 2017. [DOI: 10.1016/j.ccr.2017.03.002] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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16
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McDowell SAC, Edwards KEK. Effect of electron-donating and electron-withdrawing atoms on the C–H…Y hydrogen bond in model X3CH…YZ (X = B, F; YZ = BF, CO, N2) complexes. Mol Phys 2017. [DOI: 10.1080/00268976.2017.1357858] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Sean A. C. McDowell
- Department of Biological and Chemical Sciences, The University of the West Indies, Cave Hill Campus, Bridgetown, Barbados
| | - Kayrel E. K. Edwards
- Department of Biological and Chemical Sciences, The University of the West Indies, Cave Hill Campus, Bridgetown, Barbados
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17
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McDowell SA. Correlation of the bond-length change and vibrational frequency shift in model hydrogen-bonded complexes of pyrrole. Chem Phys Lett 2017. [DOI: 10.1016/j.cplett.2017.02.065] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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18
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Wang C, Danovich D, Shaik S, Mo Y. A Unified Theory for the Blue- and Red-Shifting Phenomena in Hydrogen and Halogen Bonds. J Chem Theory Comput 2017; 13:1626-1637. [DOI: 10.1021/acs.jctc.6b01133] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Changwei Wang
- Department
of Chemistry, School of Science, China University of Petroleum (East China), Changjiangxi Road 66, 266580 Tsingtao, China
| | - David Danovich
- Institute
of Chemistry and Lise Meitner Minerva Center for Computational Quantum
Chemistry, The Hebrew University, Jerusalem 91904, Israel
| | - Sason Shaik
- Institute
of Chemistry and Lise Meitner Minerva Center for Computational Quantum
Chemistry, The Hebrew University, Jerusalem 91904, Israel
| | - Yirong Mo
- Department
of Chemistry, Western Michigan University, Kalamazoo, Michigan 49008, United States
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19
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Schneider SH, Kratochvil HT, Zanni MT, Boxer SG. Solvent-Independent Anharmonicity for Carbonyl Oscillators. J Phys Chem B 2017; 121:2331-2338. [PMID: 28225620 DOI: 10.1021/acs.jpcb.7b00537] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The physical origins of vibrational frequency shifts have been extensively studied in order to understand noncovalent intermolecular interactions in the condensed phase. In the case of carbonyls, vibrational solvatochromism, MD simulations, and vibrational Stark spectroscopy suggest that the frequency shifts observed in simple solvents arise predominately from the environment's electric field due to the vibrational Stark effect. This is contrary to many previously invoked descriptions of vibrational frequency shifts, such as bond polarization, whereby the bond's force constant and/or partial nuclear charges are altered due to the environment, often illustrated in terms of favored resonance structures. Here we test these hypotheses using vibrational solvatochromism as measured using 2D IR to assess the solvent dependence of the bond anharmonicity. These results indicate that the carbonyl bond's anharmonicity is independent of solvent as tested using hexanes, DMSO, and D2O and is supported by simulated 2D spectra. In support of the linear vibrational Stark effect, these 2D IR measurements are consistent with the assertion that the Stark tuning rate is unperturbed by the electric field generated by both hydrogen and non-hydrogen bonding environments and further extends the general applicability of carbonyl probes for studying intermolecular interactions.
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Affiliation(s)
- Samuel H Schneider
- Department of Chemistry, Stanford University , Stanford, California 94305-5012, United States
| | - Huong T Kratochvil
- Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Martin T Zanni
- Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Steven G Boxer
- Department of Chemistry, Stanford University , Stanford, California 94305-5012, United States
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20
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Bakker DJ, Dey A, Tabor DP, Ong Q, Mahé J, Gaigeot MP, Sibert EL, Rijs AM. Fingerprints of inter- and intramolecular hydrogen bonding in saligenin–water clusters revealed by mid- and far-infrared spectroscopy. Phys Chem Chem Phys 2017; 19:20343-20356. [DOI: 10.1039/c7cp01951c] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Saligenin (2-(hydroxymethyl)phenol) exhibits both strong and weak intramolecular electrostatic interactions.
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Affiliation(s)
- Daniël J. Bakker
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- 6525 ED Nijmegen
- The Netherlands
| | - Arghya Dey
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- 6525 ED Nijmegen
- The Netherlands
| | - Daniel P. Tabor
- Department of Chemistry and Theoretical Chemistry Institute
- University of Wisconsin-Madison
- Madison
- USA
| | - Qin Ong
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- 6525 ED Nijmegen
- The Netherlands
| | - Jérôme Mahé
- LAMBE CNRS UMR8587
- Université d'Evry val d'Essonne
- Blvd F. Mitterrand
- Bât Maupertuis
- France
| | - Marie-Pierre Gaigeot
- LAMBE CNRS UMR8587
- Université d'Evry val d'Essonne
- Blvd F. Mitterrand
- Bât Maupertuis
- France
| | - Edwin L. Sibert
- Department of Chemistry and Theoretical Chemistry Institute
- University of Wisconsin-Madison
- Madison
- USA
| | - Anouk M. Rijs
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- 6525 ED Nijmegen
- The Netherlands
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21
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Kumar Deb D, Sarkar B. Theoretical investigation of gas-phase molecular complex formation between 2-hydroxy thiophenol and a water molecule. Phys Chem Chem Phys 2017; 19:2466-2478. [DOI: 10.1039/c6cp08442g] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A systematic study of the interaction energies and hydrogen bonding interaction of a gas-phase molecular complex between 2-hydroxy thiophenol and a water molecule.
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Affiliation(s)
- Debojit Kumar Deb
- Department of Chemistry
- Centre for Advanced Studies
- North-Eastern Hill University
- Shillong 793022
- India
| | - Biplab Sarkar
- Department of Chemistry
- Centre for Advanced Studies
- North-Eastern Hill University
- Shillong 793022
- India
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22
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Impact of deformation energy on the hydrogen bonding interactions in gas phase 3-X catechol⋯H2O complexes (X = H, F, Cl, Br): The effect of approach of a water molecule. Chem Phys 2016. [DOI: 10.1016/j.chemphys.2016.03.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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23
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Simultaneous interactions of amphoteric halogen in XY (X = Cl, Br and Y = F, Cl, Br) with C and O atoms of CO 2 in ring-shaped CO 2 ·X(Y)·CO 2 complexes. COMPUT THEOR CHEM 2016. [DOI: 10.1016/j.comptc.2015.11.023] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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24
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Błasiak B, Cho M. Vibrational solvatochromism. II. A first-principle theory of solvation-induced vibrational frequency shift based on effective fragment potential method. J Chem Phys 2015; 140:164107. [PMID: 24784253 DOI: 10.1063/1.4872040] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Vibrational solvatochromism is a solvation-induced effect on fundamental vibrational frequencies of molecules in solutions. Here we present a detailed first-principle coarse-grained theory of vibrational solvatochromism, which is an extension of our previous work [B. Błasiak, H. Lee, and M. Cho, J. Chem. Phys. 139(4), 044111 (2013)] by taking into account electrostatic, exchange-repulsion, polarization, and charge-transfer interactions. By applying our theory to the model N-methylacetamide-water clusters, solute-solvent interaction-induced effects on amide I vibrational frequency are fully elucidated at Hartree-Fock level. Although the electrostatic interaction between distributed multipole moments of solute and solvent molecules plays the dominant role, the contributions from exchange repulsion and induced dipole-electric field interactions are found to be of comparable importance in short distance range, whereas the charge-transfer effect is negligible. The overall frequency shifts calculated by taking into account the contributions of electrostatics, exchange-repulsion, and polarization terms are in quantitative agreement with ab initio results obtained at the Hartree-Fock level of theory.
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Affiliation(s)
- Bartosz Błasiak
- Department of Chemistry, Korea University, Seoul 136-701, South Korea
| | - Minhaeng Cho
- Department of Chemistry, Korea University, Seoul 136-701, South Korea
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25
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Fantuzzi F, Cardozo TM, Nascimento MAC. Nature of the chemical bond and origin of the inverted dipole moment in boron fluoride: a generalized valence bond approach. J Phys Chem A 2015; 119:5335-43. [PMID: 25531385 DOI: 10.1021/jp510085r] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The generalized product function energy partitioning (GPF-EP) method has been applied to investigate the nature of the chemical bond and the origin of the inverted dipole moment of the BF molecule. The calculations were carried out with GPF wave functions treating all of the core electrons as a single Hartree-Fock group and the valence electrons at the generalized valence bond perfect-pairing (GVB-PP) or full GVB levels, with the cc-pVTZ basis set. The results show that the chemical structure of both X (1)Σ(+) and a (3)Π states is composed of a single bond. The lower dissociation energy of the excited state is attributed to a stabilizing intraatomic singlet coupling involving the B 2sp-like lobe orbitals after bond dissociation. An increase of electron density on the B atom caused by the reorientation of the boron 2sp-like lobe orbitals is identified as the main responsible effect for the electric dipole inversion in the ground state of BF. Finally, it is shown that π back-bonding from fluorine to boron plays a minor role in the electron density displacement to the bonding region in both states. Moreover, this effect is associated with changes in the quasi-classical component of the electron density only and does not contribute to covalency in either of the states. Therefore, at least for the case of the BF molecule, the term back-bonding is misleading, since it does not contribute to the bond formation.
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Affiliation(s)
- Felipe Fantuzzi
- Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro RJ 21941-909, Brazil
| | - Thiago Messias Cardozo
- Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro RJ 21941-909, Brazil
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26
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Pandey P. Evidence of blue-shifting N–H⋯N hydrogen bonding despite elongation of the N–H bond. RSC Adv 2015. [DOI: 10.1039/c5ra17309d] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
N–H⋯N hydrogen bonding between pyrrole and N2 results blue shift of νN–H accompanied by an increase in the N–H bond length.
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27
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Zabardasti A, Goudarziafshar H, Salehnassaj M, Oliveira BG. A computational study of hydrogen bonds in intermolecular systems of high complexity: arachno-pentaborane(11)···Y with Y = O2 and N2. J Mol Model 2014; 20:2403. [DOI: 10.1007/s00894-014-2403-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Accepted: 07/28/2014] [Indexed: 11/29/2022]
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28
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Keinan S, Pines D, Kiefer PM, Hynes JT, Pines E. Solvent-Induced O–H Vibration Red-Shifts of Oxygen-Acids in Hydrogen-Bonded O–H···Base Complexes. J Phys Chem B 2014; 119:679-92. [DOI: 10.1021/jp502553r] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sharon Keinan
- Department
of Chemistry, Ben-Gurion University of the Negev, P.O. Box 653, Beer-Sheva, 84105, Israel
| | - Dina Pines
- Department
of Chemistry, Ben-Gurion University of the Negev, P.O. Box 653, Beer-Sheva, 84105, Israel
| | - Philip M. Kiefer
- Department
of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309-0215, United States
| | - James T. Hynes
- Department
of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309-0215, United States
- Chemistry
Department, École Normale Supérieure, UMR ENS-CNRS-UPMC 8640, 24 rue Lhomond, 75005 Paris, France
| | - Ehud Pines
- Department
of Chemistry, Ben-Gurion University of the Negev, P.O. Box 653, Beer-Sheva, 84105, Israel
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29
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Kiefer PM, Pines E, Pines D, Hynes JT. Solvent-Induced Red-Shifts for the Proton Stretch Vibrational Frequency in a Hydrogen-Bonded Complex. 1. A Valence Bond-Based Theoretical Approach. J Phys Chem B 2014; 118:8330-51. [DOI: 10.1021/jp501815j] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Philip M. Kiefer
- Department
of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309-0215, United States
| | - Ehud Pines
- Department
of Chemistry, Ben-Gurion University of the Negev, P.O. Box 653, Be’er
Sheva, 84105, Israel
| | - Dina Pines
- Department
of Chemistry, Ben-Gurion University of the Negev, P.O. Box 653, Be’er
Sheva, 84105, Israel
| | - James T. Hynes
- Department
of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309-0215, United States
- Chemistry
Department, École Normale Supérieure, UMR ENS-CNRS-UPMC 8640, 24 rue Lhomond, 75005 Paris, France
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30
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Mo Y, Wang C, Guan L, Braïda B, Hiberty PC, Wu W. On the Nature of Blueshifting Hydrogen Bonds. Chemistry 2014; 20:8444-52. [DOI: 10.1002/chem.201402189] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Indexed: 11/09/2022]
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31
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Błasiak B, Lee H, Cho M. Vibrational solvatochromism: towards systematic approach to modeling solvation phenomena. J Chem Phys 2014; 139:044111. [PMID: 23901964 DOI: 10.1063/1.4816041] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Vibrational solvatochromic frequency shift of IR probe is an effect of interaction between local electric field and IR probe in condensed phases. Despite prolonged efforts to develop empirical maps for vibrational frequency shifts and transition dipoles of IR probes, a systematic approach to ab initio calculation of vibrational solvatochromic charges and multipoles has not been developed. Here, we report on density functional theory (DFT) calculations of N-methylacetamide (NMA) frequency shifts using implicit and coarse-grained models. The solvatochromic infrared spectral shifts are estimated based on the distributed multipole analysis of electronic densities calculated for gas-phase equilibrium structure of NMA. Thus obtained distributed solvatochromic multipole parameters are used to calculate the amide I vibrational frequency shifts of NMA in water clusters that mimic the instantaneous configurations of the liquid water. Our results indicate that the spectral shifts are primarily electrostatic in nature and can be quantitatively reproduced using the proposed model with semi-quantitative accuracy when compared to the corresponding DFT results.
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Affiliation(s)
- Bartosz Błasiak
- Department of Chemistry, Korea University, Seoul 136-701, South Korea
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32
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Zhao YY, Tsuchida E, Choe YK, Ikeshoji T, Barique MA, Ohira A. Ab initio studies on the proton dissociation and infrared spectra of sulfonated poly(ether ether ketone) (SPEEK) membranes. Phys Chem Chem Phys 2014; 16:1041-9. [DOI: 10.1039/c3cp53146e] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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33
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Rivera-Rivera LA, McElmurry BA, Scott KW, Lucchese RR, Bevan JW. The Badger–Bauer Rule Revisited: Correlation of Proper Blue Frequency Shifts in the OC Hydrogen Acceptor with Morphed Hydrogen Bond Dissociation Energies in OC–HX (X = F, Cl, Br, I, CN, CCH). J Phys Chem A 2013; 117:8477-83. [DOI: 10.1021/jp4058516] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Luis A. Rivera-Rivera
- Department of Chemistry, Texas A&M University, College Station, Texas 77843-3255, United States
| | - Blake A. McElmurry
- Department of Chemistry, Texas A&M University, College Station, Texas 77843-3255, United States
| | - Kevin W. Scott
- Department of Chemistry, Texas A&M University, College Station, Texas 77843-3255, United States
| | - Robert R. Lucchese
- Department of Chemistry, Texas A&M University, College Station, Texas 77843-3255, United States
| | - John W. Bevan
- Department of Chemistry, Texas A&M University, College Station, Texas 77843-3255, United States
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34
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Magoulas I, Kalemos A, Mavridis A. An ab initio study of the electronic structure of BF and BF+. J Chem Phys 2013; 138:104312. [DOI: 10.1063/1.4793738] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
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35
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Studies of low-frequency intermolecular hydrogen-bonded vibrations using a continuous supersonic slit jet mid-infrared quantum cascade laser spectrometer. Chem Phys 2012. [DOI: 10.1016/j.chemphys.2012.09.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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36
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Tsuzuki S, Uchimaru T, Mikami M. Magnitude of CH/O interactions between carbohydrate and water. Theor Chem Acc 2012. [DOI: 10.1007/s00214-012-1192-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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37
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Inagaki S, Murai H, Takeuchi T. Theory of electron localization and its application to blue-shifting hydrogen bonds. Phys Chem Chem Phys 2012; 14:2008-14. [DOI: 10.1039/c2cp23047j] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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38
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39
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Xiao D, Prémont-Schwarz M, Nibbering ETJ, Batista VS. Ultrafast vibrational frequency shifts induced by electronic excitations: naphthols in low dielectric media. J Phys Chem A 2011; 116:2775-90. [PMID: 22044113 DOI: 10.1021/jp208426v] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We study the solvent-induced frequency shifts of the OH-stretching mode of 1-naphthol and 2-naphthol in nonpolar/weakly polar solvents, subject to electronic excitation, with ultrafast UV/mid-infrared pump-probe spectroscopy and theoretical modeling based on Pullin's perturbative treatment of vibrational solvatochromic effects. The model is parametrized at the density functional theory (DFT) level, including the B3LYP/TZVP and TD-B3LYP/TZVP descriptions, for the naphthol chromophores in the S(0)- and (1)L(b)-states and accounts for both the static and the optical dielectric response of the solvent on time scales comparable to that of the OH-stretching vibrational motions. The favorable comparison between experimental and theoretical values of the solvent-induced vibrational frequency shifts suggests that the ultrafast dielectric response of the solvent contributes predominantly to the solvatochromic shifts in solvents of moderate polarity where specific solute-solvent interactions are absent.
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Affiliation(s)
- Dequan Xiao
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, Connecticut 06520-8107, USA
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40
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McDowell SA, David Buckingham A. Theoretical studies of nickel atoms and nickel(II) ions coordinated with CO and BF ligands. Chem Phys Lett 2011. [DOI: 10.1016/j.cplett.2011.09.091] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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41
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Prémont-Schwarz M, Xiao D, Batista VS, Nibbering ETJ. The O-H stretching mode of a prototypical photoacid as a local dielectric probe. J Phys Chem A 2011; 115:10511-6. [PMID: 21851092 DOI: 10.1021/jp207642k] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
We investigate the OH stretch vibrational frequency shifts of a prototype photoacid, 2-naphthol (2N), when dissolved in solvents of low polarity. We combine femtosecond mid-infrared spectroscopy and a theoretical model based on the Pullin-van der Zwan-Hynes perturbative approach to explore vibrational solvatochromic effects in the ground S(0) and the first electronically excited (1)L(b) states. The model is parametrized using density functional theory (DFT), at the B3LYP/TZVP and TD-B3LYP/TZVP levels for the 2N chromophore in the S(0) and (1)L(b) states, respectively. From the agreement between experiment and theory we conclude that vibrational solvatochromic effects are dominated by the instantaneous dielectric response of the solvent, while time-dependent nuclear rearrangements are of secondary importance.
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Affiliation(s)
- Mirabelle Prémont-Schwarz
- Max Born Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Max Born Strasse 2A, D-12489 Berlin, Germany
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42
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Wang W, Zhang Y, Ji B, Tian A. On the correlation between bond-length change and vibrational frequency shift in halogen-bonded complexes. J Chem Phys 2011; 134:224303. [DOI: 10.1063/1.3599050] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
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43
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Scheiner S. Weak H-bonds. Comparisons of CH···O to NH···O in proteins and PH···N to direct P···N interactions. Phys Chem Chem Phys 2011; 13:13860-72. [PMID: 21573303 DOI: 10.1039/c1cp20427k] [Citation(s) in RCA: 153] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Whereas CH···O H-bonds are usually weaker than interpeptide NH···O H-bonds, this is not necessarily the case within proteins. The nominally weaker CH···O are surprisingly strong, comparable to, and in some cases stronger than, the NH···O H-bonds in the context of the forces that hold together the adjacent strands in protein β-sheets. The peptide NH is greatly weakened as proton donor in certain conformations of the protein backbone, particularly extended structures, and forms correspondingly weaker H-bonds. The PH group is a weak proton donor, but will form PH···N H-bonds. However, there is a stronger interaction in which P can engage, in which the P atom, not the H, directly approaches the N electron donor to establish a direct P···N interaction. This approach is stabilized by the same sort of electron transfer from the N lone pair to the P-H σ* antibond that characterizes the PH···N H-bond.
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Affiliation(s)
- Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT 84322-0300, USA.
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44
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Wang W, Wang D, Zhang Y, Ji B, Tian A. Hydrogen bond and halogen bond inside the carbon nanotube. J Chem Phys 2011; 134:054317. [PMID: 21303130 DOI: 10.1063/1.3549572] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Weizhou Wang
- College of Chemistry and Chemical Engineering, Luoyang Normal University, Luoyang 471022, China.
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45
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Cao LJ, Li AY, Ji HB, Xu L, Zhang Y. Theoretical study on the ring stretching modes of pyridine in the hydrogen bonding with H2O, HCONH2 and CH3COOH. ACTA ACUST UNITED AC 2010. [DOI: 10.1016/j.theochem.2010.08.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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46
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McDowell SAC, Marcellin RC. A comparative computational study of hydrogen and lithium-bonded complexes. J Chem Phys 2010; 133:144307. [DOI: 10.1063/1.3494601] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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47
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48
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Mukhopadhyay A, Pandey P, Chakraborty T. Blue- and Red-Shifting CH···O Hydrogen Bonded Complexes between Haloforms and Ethers: Correlation of Donor νC−H Spectral Shifts with C−O−C Angular Strain of the Acceptors. J Phys Chem A 2010; 114:5026-33. [PMID: 20334425 DOI: 10.1021/jp100524q] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Anamika Mukhopadhyay
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Prasenjit Pandey
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Tapas Chakraborty
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
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49
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Kumar RM, Elango M, Subramanian V. Carbohydrate-Aromatic Interactions: The Role of Curvature on XH···π Interactions. J Phys Chem A 2010; 114:4313-24. [DOI: 10.1021/jp907547f] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- R. Mahesh Kumar
- Chemical Laboratory, Central Leather Research Institute, Council of Scientific and Industrial Research, Adyar, Chennai 600 020, India
| | - M. Elango
- Chemical Laboratory, Central Leather Research Institute, Council of Scientific and Industrial Research, Adyar, Chennai 600 020, India
| | - V. Subramanian
- Chemical Laboratory, Central Leather Research Institute, Council of Scientific and Industrial Research, Adyar, Chennai 600 020, India
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McDowell SAC, Buckingham AD. Cooperative and diminutive hydrogen bonding in Y⋯HCN⋯HCN and NCH⋯Y⋯HCN trimers (Y=BF,CO,N2). J Chem Phys 2010; 132:064303. [PMID: 20151739 DOI: 10.1063/1.3297894] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Affiliation(s)
- Sean A C McDowell
- Department of Biological and Chemical Sciences, The University of the West Indies, Cave Hill Campus, P.O. Box 64, Bridgetown, Barbados.
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