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Tajouo Tela H, Quintas-Sánchez E, Dubernet ML, Scribano Y, Dawes R, Gatti F, Ndengué S. Rovibrational states calculations of the H 2O-HCN heterodimer with the multiconfiguration time dependent Hartree method. Phys Chem Chem Phys 2023; 25:31813-31824. [PMID: 37966067 DOI: 10.1039/d3cp03225f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
Water and hydrogen cyanide are two of the most common species in space and the atmosphere with the ability of binding to form dimers such as H2O-HCN. In the literature, while calculations characterizing various properties of the H2O-HCN cluster (equilibrium distance, vibrational frequencies and rotational constants) have been done in the past, extensive calculations of the rovibrational states of this system using a reliable quantum dynamical approach have yet to be reported. In this work, we intend to mend that by performing the first calculation of the rovibrational states of the H2O-HCN van der Waals complex on a recently developed potential energy surface. We use the block improved relaxation procedure implemented in the Heidelberg MultiConfiguration Time-Dependent Hartree (MCTDH) package to compute the states of the H2O-HCN isomer, from which we extract the transition frequencies and rotational constants of the complex. We further adapt an approach first suggested by Wang and Carrington-and supported here by analysis routines of the Heidelberg MCTDH package-to properly characterize the computed rovibrational states. The subsequent assignment of rovibrational states was done by theoretical analysis and visual inspection of the wavefunctions. Our simulations provide a Zero Point Energy (ZPE) and intermolecular vibrational frequencies in good agreement with past ab initio calculations. The transition frequencies and rotational constants obtained from our simulations match well with the available experimental data. This work has the broad aim to propose the MCTDH approach as a reliable option to compute and characterize rovibrational states of van der Waals complexes such as the current one.
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Affiliation(s)
- Hervé Tajouo Tela
- ICTP-East African Institute for Fundamental Research, University of Rwanda, Kigali, Rwanda.
| | - Ernesto Quintas-Sánchez
- Department of Chemistry, Missouri University of Science and Technology, 65409 Rolla, Missouri, USA
| | - Marie-Lise Dubernet
- LERMA, Observatoire de Paris, PSL Research University, CNRS, Sorbonne University, UPMC Univ Paris 06, 75014 Paris, France
| | - Yohann Scribano
- Laboratoire Univers et Particules de Montpellier, UMR-CNRS 5299, Université de Montpellier, Place Eugène Bataillon, 34095 Montpellier, France
| | - Richard Dawes
- Department of Chemistry, Missouri University of Science and Technology, 65409 Rolla, Missouri, USA
| | - Fabien Gatti
- Institut de Sciences Moleculaires d'Orsay, UMR 8214, Université Paris-Sud - Université Paris-Saclay, 91405 Orsay, France
| | - Steve Ndengué
- ICTP-East African Institute for Fundamental Research, University of Rwanda, Kigali, Rwanda.
- Department of Physics, Trinity College, 06106 Hartford, Connecticut, USA
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Vindel-Zandbergen P, Kȩdziera D, Żółtowski M, Kłos J, Żuchowski P, Felker PM, Lique F, Bačić Z. H2O-HCN complex: A new potential energy surface and intermolecular rovibrational states from rigorous quantum calculations. J Chem Phys 2023; 159:174302. [PMID: 37909452 DOI: 10.1063/5.0173751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 10/13/2023] [Indexed: 11/03/2023] Open
Abstract
In this work the H2O-HCN complex is quantitatively characterized in two ways. First, we report a new rigid-monomer 5D intermolecular potential energy surface (PES) for this complex, calculated using the symmetry-adapted perturbation theory based on density functional theory method. The PES is based on 2833 ab initio points computed employing the aug-cc-pVQZ basis set, utilizing the autoPES code, which provides a site-site analytical fit with the long-range region given by perturbation theory. Next, we present the results of the quantum 5D calculations of the fully coupled intermolecular rovibrational states of the H2O-HCN complex for the total angular momentum J values of 0, 1, and 2, performed on the new PES. These calculations rely on the quantum bound-state methodology developed by us recently and applied to a variety of noncovalently bound binary molecular complexes. The vibrationally averaged ground-state geometry of H2O-HCN determined from the quantum 5D calculations agrees very well with that from the microwave spectroscopic measurements. In addition, the computed ground-state rotational transition frequencies, as well as the B and C rotational constants calculated for the ground state of the complex, are in excellent agreement with the experimental values. The assignment of the calculated intermolecular vibrational states of the H2O-HCN complex is surprisingly challenging. It turns out that only the excitations of the intermolecular stretch mode can be assigned with confidence. The coupling among the angular degrees of freedom (DOFs) of the complex is unusually strong, and as a result most of the excited intermolecular states are unassigned. On the other hand, the coupling of the radial, intermolecular stretch mode and the angular DOFs is weak, allowing straightforward assignment of the excitation of the former.
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Affiliation(s)
| | - Dariusz Kȩdziera
- Faculty of Chemistry, Nicolaus Copernicus University in Toruń, ul. Gagarina 7, 87-100 Toruń, Poland
| | - Michał Żółtowski
- University of Rennes, CNRS, IPR (Institut de Physique de Rennes) - UMR 6251, F-35000 Rennes, France
- LOMC - UMR 6294, CNRS-Université du Havre, 25 rue Philippe Lebon, BP1123, 76 063 Le Havre cedex, France
| | - Jacek Kłos
- Joint Quantum Institute, University of Maryland, College Park, Maryland 20742, USA
| | - Piotr Żuchowski
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University, ul. Grudziądzka 5, 87-100 Toruń, Poland
| | - Peter M Felker
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, USA
| | - François Lique
- University of Rennes, CNRS, IPR (Institut de Physique de Rennes) - UMR 6251, F-35000 Rennes, France
| | - Zlatko Bačić
- Department of Chemistry, New York University, New York, New York 10003, USA
- Simons Center for Computational Physical Chemistry at New York University, New York, New York 10003, USA
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, 3663 Zhongshan Road North, Shanghai 200062, China
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Darla N, Sharma D, Sitha S. Formation of Formamide from HCN + H 2O: A Computational Study on the Roles of a Second H 2O as a Catalyst, as a Spectator, and as a Reactant. J Phys Chem A 2019; 124:165-175. [PMID: 31820987 DOI: 10.1021/acs.jpca.9b09924] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Formamide (NH2CHO), being the smallest and fundamental building block of life (with a peptide linkage), has recently been able to attract much interests, in the field of astrochemistry, astrophysics, and astrobiology. In this work, using quantum mechanical computations, reactions between HCN and H2O, leading to the formation of formamide, have been analyzed. For the first time, an alternative and competing reaction channel, which proceeds via a geminal diol intermediate, for the formation of formamide, has been proposed. In this alternative channel, an extra water molecule (second H2O) was found to be acting as a reactant, in the second step of the reaction path. Effects of second H2O molecule in the reaction paths, providing catalytic assistance to the reaction or behaving like a spectator (concept is introduced for the first time for this reaction), have also been analyzed. Usefulness of spectator behavior is highlighted for the reactions happening on the rigid water-ice surfaces, where the water-ice may not be getting involved for any catalytic assistance. In light of catalytic assistances provided by the second H2O, prominent effects in reducing the barrier heights drastically (even for the second step of the reaction, the barrier height was found to be below the reactants), through a hydrogen relay transport mechanism, were observed. In addition to the mechanism studies, interstellar feasibilities of all the reaction channels and their significances are discussed in detail.
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Affiliation(s)
- Nagasuneetha Darla
- Department of Chemical Sciences , University of Johannesburg , P.O. Box 524, Auckland Park, Johannesburg , South Africa 2006
| | - Divya Sharma
- Department of Chemical Sciences , University of Johannesburg , P.O. Box 524, Auckland Park, Johannesburg , South Africa 2006
| | - Sanyasi Sitha
- Department of Chemical Sciences , University of Johannesburg , P.O. Box 524, Auckland Park, Johannesburg , South Africa 2006
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Chaudhuri P, Ducati LC, Ghosh A. Spin–spin coupling constants in linear substituted HCN clusters. Mol Phys 2019. [DOI: 10.1080/00268976.2018.1537528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Puspitapallab Chaudhuri
- Department of Physics, Federal University of Amazonas, Manaus, Brazil
- Institute of Physics, University of São Paulo, São Paulo, Brazil
| | - Lucas C. Ducati
- Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - Angsula Ghosh
- Department of Physics, Federal University of Amazonas, Manaus, Brazil
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Sánchez EQ, Dubernet ML. Theoretical study of HCN-water interaction: five dimensional potential energy surfaces. Phys Chem Chem Phys 2017; 19:6849-6860. [PMID: 28218316 DOI: 10.1039/c6cp07894j] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A new five-dimensional potential energy surface is calculated at the coupled-cluster CCSD(T) level of theory for the HCN-water system, treating both monomers as rigid rotors. The associated methodology, which combines extensive ab initio calculations of moderate accuracy (CCSD(T)/AVDZ) and a fitting procedure involving a much lower angular coverage with more accurate ab initio calculations (CCSD(T)/CBS), is described in detail. This methodology provides a time-saving approach to compute quantitatively accurate potential energy surfaces with reasonable computational effort. Our potential reproduces the main features reported in the literature, and will allow us to perform the first quantum and semi-classical simulations of the collisional dynamic on this system.
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Affiliation(s)
- Ernesto Quintas Sánchez
- LERMA, Observatoire de Paris, PSL Research University, CNRS, Sorbonne University, UPMC Univ Paris 06, 5 Place Janssen, 92190 Meudon, France.
| | - Marie-Lise Dubernet
- LERMA, Observatoire de Paris, PSL Research University, CNRS, Sorbonne University, UPMC Univ Paris 06, 5 Place Janssen, 92190 Meudon, France.
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Deb P, Haldar T, Kashid SM, Banerjee S, Chakrabarty S, Bagchi S. Correlating Nitrile IR Frequencies to Local Electrostatics Quantifies Noncovalent Interactions of Peptides and Proteins. J Phys Chem B 2016; 120:4034-46. [DOI: 10.1021/acs.jpcb.6b02732] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Pranab Deb
- Physical and Materials Chemistry
Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India
| | - Tapas Haldar
- Physical and Materials Chemistry
Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India
| | - Somnath M Kashid
- Physical and Materials Chemistry
Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India
| | - Subhrashis Banerjee
- Physical and Materials Chemistry
Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India
| | - Suman Chakrabarty
- Physical and Materials Chemistry
Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India
| | - Sayan Bagchi
- Physical and Materials Chemistry
Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India
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8
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da Silva AM, Chakrabarty S, Chaudhuri P. Hydrogen-bonded glycine–HCN complexes in gas phase: structure, energetics, electric properties and cooperativity. Mol Phys 2014. [DOI: 10.1080/00268976.2014.953013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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da Silva AM, Ghosh A, Chaudhuri P. Effect of Hydrogen Bond Formation on the NMR Properties of Glycine–HCN Complexes. J Phys Chem A 2013; 117:10274-85. [DOI: 10.1021/jp4056818] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Arnaldo Machado da Silva
- Departamento
de Física, Universidade Federal do Amazonas, 69077-000 Manaus, AM, Brazil
- Departamento
de Física, Universidade Federal de São Carlos, São Paulo 13565-905, Brazil
| | - Angsula Ghosh
- Departamento
de Física, Universidade Federal do Amazonas, 69077-000 Manaus, AM, Brazil
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WANG CUIHONG, ZHANG RUIQIN, LIN ZIJING. A COMPARATIVE STUDY ON INTERMOLECULAR HYDROGEN BOND INTERACTIONS IN MOLECULAR DIMERS USING DIFFERENT LEVELS OF COMPUTATIONAL METHODS. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2012. [DOI: 10.1142/s0219633612500836] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Hydrogen bond interactions in biological systems are important scientific issues but are challenging for their theoretical determinations at quantum-mechanical level of theory. Due to the different approximations, the available theoretical approaches often predict diverse hydrogen bond lengths and strengths. In this work, we evaluated the reliabilities of a number of widely used theoretical approaches including HF, SVWN, BLYP, PW91, B3LYP, BH and HLYP, B97D, M06L, MP2, and DFTB-D in studying hydrogen bonding, by calculating the hydrogen bond lengths and binding energies of 23 dimers formed by HCOOH , NH3 and Glycine. We also compared the effects of STO-3G, 6-31+G**, 6-311++G** and 6-311++G(2df,2p) basis sets on the results. Our result shows that, M06L, B3LYP and BHandHLYP methods can predict accurate dimer structures with a moderate basis set. Moreover, DFTB-D also gives reasonably reliable results with high efficiency and satisfactory precision, being a good choice for studying complex structures which contain hydrogen bonds.
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Affiliation(s)
- CUIHONG WANG
- Department of Physics, University of Science and Technology of China, Hefei 230026, China
- Department of Physics and Materials Sciences, City University of Hong Kong, Hong Kong S.A.R., China
- USTC-CityU Joint Advanced Research Centre, Suzhou 215123, China
| | - RUIQIN ZHANG
- Department of Physics and Materials Sciences, City University of Hong Kong, Hong Kong S.A.R., China
| | - ZIJING LIN
- Department of Physics, University of Science and Technology of China, Hefei 230026, China
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11
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LANKAU TIMM, WU YUCHUNG, ZOU JIANWEI, YU CHINHUI. THE COOPERATIVITY BETWEEN HYDROGEN AND HALOGEN BONDS. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2011. [DOI: 10.1142/s0219633608003563] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The cooperativity between hydrogen bonds and halogen bonds in X–HCN–Y ( X: C2H2, H2O, NH3, HCI, HCN, HF; Y: HF, BrF, Br2 is analyzed with MP2/6-311++G(d, p) and DFT/6-311++G(d, p) calculations using the B3LYP and mPW1PW91 hybrid functionals. The results from the quantum chemical calculations are typically clustered in groups according to the Y-ligand. By choosing the X–HCN–HF group as reference it is possible to describe the interaction between the hydrogen and the halogen bond with a two-parameter model. The value of the first parameter of the model describes the contribution of the X -ligand to the interbond cooperativity in the reference cluster. The second parameter of our model quantifies the changes in interbond cooperativity upon varying the Y -ligand. This simple model can be used to predict the cooperativity in X–HCN–Y trimers with reasonable accuracy and thereby to organize the results systematically. It is further shown that the conclusions drawn from this ordering scheme are independent from the computational method and thereby generally applicable.
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Affiliation(s)
- TIMM LANKAU
- Department of Chemistry, National Tsing Hua University, 101 Kuang Fu Road Sec. 2, Hsin Chu 30013, Taiwan
| | - YU-CHUNG WU
- Department of Chemistry, National Tsing Hua University, 101 Kuang Fu Road Sec. 2, Hsin Chu 30013, Taiwan
| | - JIAN-WEI ZOU
- Department of Chemistry, National Tsing Hua University, 101 Kuang Fu Road Sec. 2, Hsin Chu 30013, Taiwan
| | - CHIN-HUI YU
- Department of Chemistry, National Tsing Hua University, 101 Kuang Fu Road Sec. 2, Hsin Chu 30013, Taiwan
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12
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Kołaski M, Zakharenko AA, Karthikeyan S, Kim KS. Structures, Energetics, and IR Spectra of Monohydrated Inorganic Acids: Ab initio and DFT Study. J Chem Theory Comput 2011; 7:3447-59. [DOI: 10.1021/ct100428z] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Maciej Kołaski
- Center for Superfunctional Materials, Department of Chemistry, Pohang University of Science and Technology, San 31, Hyojadong, Namgu, 790-784 Pohang, South Korea
| | - Aleksey A. Zakharenko
- Center for Superfunctional Materials, Department of Chemistry, Pohang University of Science and Technology, San 31, Hyojadong, Namgu, 790-784 Pohang, South Korea
| | - S. Karthikeyan
- Center for Superfunctional Materials, Department of Chemistry, Pohang University of Science and Technology, San 31, Hyojadong, Namgu, 790-784 Pohang, South Korea
| | - Kwang S. Kim
- Center for Superfunctional Materials, Department of Chemistry, Pohang University of Science and Technology, San 31, Hyojadong, Namgu, 790-784 Pohang, South Korea
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Abstract
Three different nitrile-containing amino acids, p-cyanophenylalanine, m-cyanophenylalanine, and S-cyanohomocysteine, have been introduced near the active site of the semisynthetic enzyme ribonuclease S (RNase S) to serve as probes of electrostatic fields. Vibrational Stark spectra, measured directly on the probe-modified proteins, confirm the predominance of the linear Stark tuning rate in describing the sensitivity of the nitrile stretch to external electric fields, a necessary property for interpreting observed frequency shifts as a quantitative measure of local electric fields that can be compared with simulations. The X-ray structures of these nitrile-modified RNase variants and enzymatic assays demonstrate minimal perturbation to the structure and function, respectively, by the probes and provide a context for understanding the influence of the environment on the nitrile stretching frequency. We examine the ability of simulation techniques to recapitulate the spectroscopic properties of these nitriles as a means to directly test a computational electrostatic model for proteins, specifically that in the ubiquitous Amber-99 force field. Although qualitative agreement between theory and experiment is observed for the largest shifts, substantial discrepancies are observed in some cases, highlighting the ongoing need for experimental metrics to inform the development of theoretical models of electrostatic fields in proteins.
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Affiliation(s)
- Aaron Fafarman
- Department of Chemistry Stanford University Stanford, California 94305-5080
| | - Steven G. Boxer
- Department of Chemistry Stanford University Stanford, California 94305-5080
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Jing B, Li Q, Gong B, Cheng J, Li W, Liu Z. A theoretical analysis of the weakly bound complexes HM ··· HXY (M=O and S; XY=CN and NC): comparison with H2M ··· HXY complexes. Mol Phys 2010. [DOI: 10.1080/00268976.2010.489518] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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15
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Djebra-Belmessaoud N, Nait Achour M, Berthier G, Savinelli R. A comparative theoretical study of the hydrogen bonding between cyanide or isocyanide hydrides and water. ACTA ACUST UNITED AC 2010. [DOI: 10.1016/j.theochem.2009.11.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Rudakova AV, Sekushin VN, Marinov IL, Tsyganenko AA. IR spectroscopic testing of surfaces in water ice and in icy mixtures with prussic acid or ammonia. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2009; 25:1482-1487. [PMID: 19117474 DOI: 10.1021/la802792u] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
An experimental technique is developed for spectral studies of ice films deposited at 77 K onto the ZnSe inner windows of a cell, so that the spectra could be registered in the presence of gaseous adsorbate. Pure H2O or D2O ice as well as HCN/D2O and ND3/D2O mixed icy films with different dopant/water ratios (1:10, 1:5, and 1:1) were investigated. The surface area of ice deposited at 77 K H2O estimated from adsorption measurements was about 160 m2/g. Bands of dangling hydroxyl groups disappear on raising the temperature up to 130-160 K when the changes of bulk absorption provide evidence for a phase transition from amorphous to polycrystalline ice. Surface properties of icy films were characterized by low-temperature adsorption of CO and CHF3. Insertion of small doses of HCN or ammonia does not change the acid/base strength of dangling hydroxyl groups or coordinately unsaturated surface oxygen atoms, but it changes the proportion between the concentrations of these sites as compared with pure water ice. For high dopant concentrations, the dangling hydroxyls were not observed, and the dominant adsorption sites for CO are likely to be the unsaturated oxygen atoms, while serious structural changes occur in the bulk of ices.
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Affiliation(s)
- Aida V Rudakova
- Department of Photonics, V. A. Fock Institute of Physics, St. Petersburg State University, St. Petersburg, Russia 198504
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18
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Kassaee M, Cheshmehkani A, Musavi S, Majdi M, Motamedi E. 1H-Phosphepine-benzene phosphine valence tautomerizations: Impacts of substituents at ab initio and DFT levels. ACTA ACUST UNITED AC 2008. [DOI: 10.1016/j.theochem.2008.06.025] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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19
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Rivelino R. Lewis acid-base interactions in weakly bound formaldehyde complexes with CO2, HCN, and FCN: considerations on the cooperative H-bonding effects. J Phys Chem A 2007; 112:161-5. [PMID: 18154278 DOI: 10.1021/jp7105154] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Ab initio quantum chemistry calculations reveal that HCN and mainly FCN can form Lewis acid-base complexes with formaldehyde associated with cooperative H bonds, as first noticed by Wallen et al. (Blatchford, M. A.; Raveendran, P.; Wallen, S. L. J. Am. Chem. Soc. 2002, 124, 14818-14819) for CO2-philic materials under supercritical conditions. The present results, obtained with MP2(Full)/aug-cc-pVDZ calculations, show that the degeneracy of the nu(2) mode in free HCN or FCN is removed upon complexation in the same fashion as that of CO2. The splitting of these bands along with the electron structure analysis provides substantial evidence of the interaction of electron lone pairs of the carbonyl oxygen with the electron-deficient carbon atom of the cyanides. Also, this work investigates the role of H bonds acting as additional stabilizing interactions in the complexes by performing the energetic and geometric characterization.
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Bouchoux G. Gas-phase basicities of polyfunctional molecules. Part 1: Theory and methods. MASS SPECTROMETRY REVIEWS 2007; 26:775-835. [PMID: 17854059 DOI: 10.1002/mas.20151] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
The experimental and theoretical methods of determination of gas-phase basicities, proton affinities and protonation entropies are presented in a tutorial form. Particularities and limitations of these methods when applied to polyfunctional molecules are emphasized. Structural effects during the protonation process in the gas-phase and their consequences on the corresponding thermochemistry are reviewed and classified. The role of the nature of the basic site (protonation on non-bonded electron pairs or on pi-electron systems) and of substituent effects (electrostatic and resonance) are first examined. Then, linear correlations observed between gas-phase basicities and ionization energies or substituent constants are recalled. Hydrogen bonding plays a special part in proton transfer reactions and in the protonation characteristics of polyfunctional molecules. A survey of the main properties of intermolecular and intramolecular hydrogen bonding in both neutral and protonated species is proposed. Consequences on the protonation thermochemistry, particularly of polyfunctional molecules are discussed. Finally, chemical reactions which may potentially occur inside protonated clusters during the measurement of gas-phase basicities or inside a protonated polyfunctional molecule is examined. Examples of bond dissociations with hydride or alkyl migrations, proton transport catalysis, tautomerization, cyclization, ring opening and nucleophilic substitution are presented to illustrate the potentially complex chemistry that may accompany the protonation of polyfunctional molecules.
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Affiliation(s)
- Guy Bouchoux
- Laboratoire des Mécanismes Réactionnels, Département de Chimie, Ecole Polytechnique, 91120 Palaiseau, France.
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21
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Coupeaud A, Piétri N, Aycard JP, Couturier-Tamburelli I. Water/cyanobutadiyne complexes: an infrared matrix isolation and theoretical study. Phys Chem Chem Phys 2007; 9:3985-91. [PMID: 17646887 DOI: 10.1039/b703402d] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The structures and energies of the 1:1 HC5N:H2O complexes in solid argon matrices have been investigated using FTIR spectroscopy and ab initio calculations, at the B3LYP/6-31G** and MP2/6-31G** levels of theory. Two types of 1:1 complexes are observed. The first one corresponds to the NH structure characterized by a hydrogen bond between H2O and the nitrogen of HC5N. The second corresponds to the OH form that involves a van der Waals interaction between the hydrogen of HC5N and the oxygen of water. HC5N can thus act either as an electrophile or as a nucleophile in complexes with water.
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Affiliation(s)
- Anne Coupeaud
- UMR CNRS 6633, Physique des Interactions Ioniques et Moléculaires, Equipe de Spectrométries et Dynamique Moléculaires, Université de Provence, Case 252, Centre de St-Jérôme, 13397, Marseille cedex 20, France
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