1
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Substituent effects on the halogen and pnictogen bonds characteristics in ternary complexes 4-YPhNH2···PH2F···ClX (Y = H, F, CN, CHO, NH2, CH3, NO2 and OCH3, and X = F, OH, CN, NC, FCC and NO2): A theoretical study. J CHEM SCI 2019. [DOI: 10.1007/s12039-019-1715-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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2
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Bora PL, Novák M, Novotný J, Foroutan-Nejad C, Marek R. Supramolecular Covalence in Bifurcated Chalcogen Bonding. Chemistry 2017; 23:7315-7323. [DOI: 10.1002/chem.201700179] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Indexed: 12/13/2022]
Affiliation(s)
- Pankaj Lochan Bora
- CEITEC-Central European Institute of Technology; Masaryk University; Kamenice 5 62500 Brno Czech Republic
- Department of Chemistry; Faculty of Science; Masaryk University; Kamenice 5 62500 Brno Czech Republic
| | - Martin Novák
- CEITEC-Central European Institute of Technology; Masaryk University; Kamenice 5 62500 Brno Czech Republic
- National Center for Biomolecular Research; Faculty of Science; Masaryk University; Kamenice 5 62500 Brno Czech Republic
| | - Jan Novotný
- CEITEC-Central European Institute of Technology; Masaryk University; Kamenice 5 62500 Brno Czech Republic
| | - Cina Foroutan-Nejad
- CEITEC-Central European Institute of Technology; Masaryk University; Kamenice 5 62500 Brno Czech Republic
| | - Radek Marek
- CEITEC-Central European Institute of Technology; Masaryk University; Kamenice 5 62500 Brno Czech Republic
- Department of Chemistry; Faculty of Science; Masaryk University; Kamenice 5 62500 Brno Czech Republic
- National Center for Biomolecular Research; Faculty of Science; Masaryk University; Kamenice 5 62500 Brno Czech Republic
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3
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Matczak P. Theoretical analysis of trends in hydrogen bonding involving halogen acceptors (F−At) covalently bonded to a group 14 atom (C−Pb). Mol Phys 2016. [DOI: 10.1080/00268976.2016.1268727] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Piotr Matczak
- Department of Theoretical and Structural Chemistry, Faculty of Chemistry, University of Łódź, Lodz, Poland
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4
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Riley KE, Hobza P. Investigations into the Nature of Halogen Bonding Including Symmetry Adapted Perturbation Theory Analyses. J Chem Theory Comput 2015; 4:232-42. [PMID: 26620655 DOI: 10.1021/ct700216w] [Citation(s) in RCA: 387] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
In recent years it has been recognized that, because of their unique properties, halogen bonds have tremendous potential in the development of new pharmaceutical compounds and materials. In this study we investigate the phenomenon of halogen bonding by carrying out ab initio calculations on the halomethane-formaldehyde complexes as well as the fluorine substituted FnH3-nCX···OCH2 dimers, where the halogen bonding halogens (X) are chlorine, bromine, and iodine. Coupled cluster (CCSD(T)/aug-cc-pVTZ) calculations indicate that the binding energies for these type of interactions lie in the range between -1.05 kcal/mol (H3CCl···OCH2) and -3.72 kcal/mol (F3CI···OCH2). One of the most important findings in this study is that, according to symmetry adapted perturbation theory (SAPT) analyses, halogen bonds are largely dependent on both electrostatic and dispersion type interactions. As the halogen atom involved in halogen bonding becomes larger the interaction strength for this type of interaction also gets larger and, interestingly, more electrostatic (and less dispersive) in character. Halogen bonding interactions also become stronger and more electrostatic upon substitution of (the very electronegative) fluorines onto the halomethane molecule.
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Affiliation(s)
- Kevin E Riley
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center for Biomolecules and Complex Molecular Systems, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
| | - Pavel Hobza
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center for Biomolecules and Complex Molecular Systems, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
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5
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Adluri ANS, Murphy JN, Tozer T, Rowley CN. Polarizable Force Field with a σ-Hole for Liquid and Aqueous Bromomethane. J Phys Chem B 2015; 119:13422-32. [DOI: 10.1021/acs.jpcb.5b09041] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Archita N. S. Adluri
- Department
of Chemistry, Memorial University of Newfoundland, St. John’s, Newfoundland A1B 3X7, Canada
| | - Jennifer N. Murphy
- Department
of Chemistry, Memorial University of Newfoundland, St. John’s, Newfoundland A1B 3X7, Canada
| | - Tiffany Tozer
- Department
of Chemistry, Memorial University of Newfoundland, St. John’s, Newfoundland A1B 3X7, Canada
| | - Christopher N. Rowley
- Department
of Chemistry, Memorial University of Newfoundland, St. John’s, Newfoundland A1B 3X7, Canada
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6
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Habartová A, Hormain L, Pluhařová E, Briquez S, Monnerville M, Toubin C, Roeselová M. Molecular Simulations of Halomethanes at the Air/Ice Interface. J Phys Chem A 2015; 119:10052-9. [PMID: 26334558 DOI: 10.1021/acs.jpca.5b06071] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Halogenated organics are emitted into the atmosphere from a variety of sources of both natural and anthropogenic origin. Their uptake at the surface of aerosols can affect their reactivity, for example, in processes that take part in ozone destruction due to production of reactive chlorine, bromine, and iodine radicals. Classical molecular dynamics (MD) simulations are carried out to investigate the interaction of small halomethane molecules of atmospheric relevance with a crystalline ice surface. The following halomethanes were studied: CH3Cl, CH2Cl2, CHCl3, CH3Br, CH2Br2, and CHBr3. MD simulations provide an invaluable insight into the adsorption behavior of halomethanes species. The adsorption energy is increasing as the number of halogen atoms is increasing. Moreover, brominated methanes exhibit a stronger interaction with the ice than their chlorinated analogs. Implications for the atmospheric chemistry are discussed.
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Affiliation(s)
- A Habartová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , Flemingovo nám. 2, 16610 Prague 6, Czech Republic
| | - L Hormain
- PhLAM Laboratory, UMR CNRS 8523, Université de Lille , Cité Scientifique, 59655 Villeneuve d'Ascq, France
| | - E Pluhařová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , Flemingovo nám. 2, 16610 Prague 6, Czech Republic.,Department of Chemistry, École Normale Supérieure, UMR ENS-CNRS-UPMC 8640 , 24 rue Lhomond, 75005 Paris, France
| | - S Briquez
- PhLAM Laboratory, UMR CNRS 8523, Université de Lille , Cité Scientifique, 59655 Villeneuve d'Ascq, France
| | - M Monnerville
- PhLAM Laboratory, UMR CNRS 8523, Université de Lille , Cité Scientifique, 59655 Villeneuve d'Ascq, France
| | - C Toubin
- PhLAM Laboratory, UMR CNRS 8523, Université de Lille , Cité Scientifique, 59655 Villeneuve d'Ascq, France
| | - M Roeselová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , Flemingovo nám. 2, 16610 Prague 6, Czech Republic
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7
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Interplay between halogen and chalcogen bonding in the XCl∙∙∙OCS∙∙∙NH3 (X = F, OH, NC, CN, and FCC) complex. J Mol Model 2014; 20:2458. [DOI: 10.1007/s00894-014-2458-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 09/01/2014] [Indexed: 10/24/2022]
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8
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Grinvald II, Kalagaev IY, Artemov AN, Sutyagina EA, Spirin IA. IR spectral manifestation of the association of organic liquids in a solid matrix. Russ Chem Bull 2014. [DOI: 10.1007/s11172-014-0480-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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9
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Partial hydration of n-alkyl halides at the water–vapor interface: a molecular simulation study with atmospheric implications. Theor Chem Acc 2014. [DOI: 10.1007/s00214-014-1455-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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10
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Cheng N, Liu Y, Zhang C, Liu C. A theoretical study on the halogen bonding interactions of C6F5I with a series of group 10 metal monohalides. J Mol Model 2013; 19:3821-9. [DOI: 10.1007/s00894-013-1910-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Accepted: 06/03/2013] [Indexed: 11/27/2022]
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11
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Theoretical study of the cooperativity in substituted dimethyl ethers complexed with two water molecules. Red or blue shifts of the ν(CH) vibrations? Chem Phys 2013. [DOI: 10.1016/j.chemphys.2012.10.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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12
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Abstract
The unusual interactions in organic liquids such as methane derivatives, arenes, and alkanes by the infrared (IR) method were revealed. The transformations of molecular shapes, arising from nonclassical hydrogen and dihydrogen bonds, as well as water factor provide the existence of supramolecular structures in organic fluids. The interpretation of the obtained results in terms of the quantum-chemical calculations has been suggested.
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14
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Li QZ, Li R, Liu XF, Li WZ, Cheng JB. Concerted interaction between pnicogen and halogen bonds in XCl-FH2P-NH3 (X=F, OH, CN, NC, and FCC). Chemphyschem 2012; 13:1205-12. [PMID: 22323307 DOI: 10.1002/cphc.201100860] [Citation(s) in RCA: 116] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2011] [Revised: 12/02/2011] [Indexed: 11/06/2022]
Abstract
We analyze the interplay between pnicogen-bonding and halogen-bonding interactions in the XCl-FH(2)P-NH(3) (X=F, OH, CN, NC, and FCC) complex at the MP2/aug-cc-pVTZ level. Synergetic effects are observed when pnicogen and halogen bonds coexist in the same complex. These effects are studied in terms of geometric and energetic features of the complexes. Natural bond orbital theory and Bader's theory of "atoms in molecules" are used to characterize the interactions and analyze their enhancement with varying electron density at critical points and orbital interactions. The physical nature of the interactions and the mechanism of the synergetic effects are studied using symmetry-adapted perturbation theory. By taking advantage of all the aforementioned computational methods, the present study examines how both interactions mutually influence each other.
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Affiliation(s)
- Qing-Zhong Li
- The Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Yantai University, Yantai 264005, P.R. China.
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15
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Li R, Li Q, Liu Z, Li W, Luan F, Cheng J, Gong B. Enhancing the function, non-additivity, and substitution position effect of the Li atom in the cation–π interaction and its mechanism: anab initiostudy of Li+ ··· Li-substituted benzene complexes. Mol Phys 2012. [DOI: 10.1080/00268976.2011.633107] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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16
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HE QIN, LI ZHIFENG. THEORETICAL STUDY OF THE HYDROGEN BOND CHARACTER BETWEEN THE FNO AND HO2 RADICAL. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2011. [DOI: 10.1142/s0219633610006092] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The hydrogen-bonding characters between FNO and HO2 radical are studied systematically with the MPWB1K method and 6-311++G (d, p), aug-cc-PVDZ as well as aug-cc-PVTZ basis sets. The relevant geometrical characteristics, energy properties, and the characters of the intramolecular hydrogen bonds have been reported in this work. In addition, the changes of electrostatic potential density are presented for further understanding the nature of hydrogen bonds and the preference of F atom as the hydrogen-bonding site.
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Affiliation(s)
- QIN HE
- Department of Chemistry, Tangshan Teachers College, Tangshan 063000, P. R. China
| | - ZHI-FENG LI
- College of Life Science and Chemistry, Tianshui Normal University, Tianshui 741001, P. R. China
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17
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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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18
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Characterization of PDZ domain–peptide interactions using an integrated protocol of QM/MM, PB/SA, and CFEA analyses. J Comput Aided Mol Des 2011; 25:947-58. [DOI: 10.1007/s10822-011-9474-5] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2011] [Accepted: 09/13/2011] [Indexed: 01/04/2023]
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19
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Scheiner S, Adhikari U. Abilities of Different Electron Donors (D) to Engage in a P···D Noncovalent Interaction. J Phys Chem A 2011; 115:11101-10. [DOI: 10.1021/jp2082787] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322-0300, United States
| | - Upendra Adhikari
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322-0300, United States
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20
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Li Q, Junling Z, Li R, Li W, Cheng J, Gong B. Rare gas atomic number dependence of the halogen bond in HRgF–XCCF (Rg=He, Ar, Kr; X=Cl, Br) complex. COMPUT THEOR CHEM 2011. [DOI: 10.1016/j.comptc.2011.05.027] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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21
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Li Q, Li R, Liu Z, Li W, Cheng J. Interplay between halogen bond and lithium bond in MCN-LiCN-XCCH (M = H, Li, and Na; X = Cl, Br, and I) complex: The enhancement of halogen bond by a lithium bond. J Comput Chem 2011; 32:3296-303. [DOI: 10.1002/jcc.21916] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2011] [Revised: 07/06/2011] [Accepted: 07/25/2011] [Indexed: 11/11/2022]
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22
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The role of CS₂ in CS₂/NMP mixed solvent in weakening the hydrogen bond of OH-N in coal: a DFT investigation. J Mol Model 2011; 18:921-7. [PMID: 21625896 DOI: 10.1007/s00894-011-1128-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2011] [Accepted: 05/12/2011] [Indexed: 10/18/2022]
Abstract
The interaction processes of trace amounts of N-methyl-2-pyrrolidinone (NMP), CS(2)/NMP (1:1 by volume) and pure NMP solvent with the hydrogen bond of OH⋯N in coal were constructed and simulated by density functional theory methods. The distances and bond orders between the main related atoms, and the hydrogen bond energy of OH⋯N were calculated. The calculated results show that pure NMP solvent does not weaken the hydrogen bond of OH⋯N in coal. However, trace amounts of NMP and CS(2)/NMP (1:1 by volume) have a strong capacity to weaken the hydrogen bond of OH⋯N in coal. The H2-N3 distances are elongated from 1.87 Å to 3.80 Å and 3.44 Å, the bond orders of H2-N3 all disappear, and the corresponding hydrogen bond energies of OH⋯N in coal decrease from 45.72 kJ mol(-1) to 7.06 and 11.24 kJ mol(-1), respectively. These results show that CS(2) added to pure NMP solvent plays an important role in releasing the original capacity of NMP to weaken the hydrogen bond of OH⋯N in coal, in agreement with experimental observations.
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23
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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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24
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Mohajeri A, Alipour M, Mousaee M. Halogen−Hydride Interaction between Z−X (Z = CN, NC; X = F, Cl, Br) and H−Mg−Y (Y = H, F, Cl, Br, CH3). J Phys Chem A 2011; 115:4457-66. [DOI: 10.1021/jp200689b] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Afshan Mohajeri
- Department of Chemistry, College of Sciences, Shiraz University, Shiraz 71454, Iran
| | - Mojtaba Alipour
- Department of Chemistry, College of Sciences, Shiraz University, Shiraz 71454, Iran
| | - Mahboubeh Mousaee
- Department of Chemistry, College of Sciences, Shiraz University, Shiraz 71454, Iran
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25
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Competition and cooperativity between hydrogen bond and halogen bond in HNC⋯(HOBr)n and (HNC)n⋯HOBr (n=1 and 2) systems. COMPUT THEOR CHEM 2011. [DOI: 10.1016/j.comptc.2010.11.006] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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26
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Wang W, Ji B, Zhang Y. Chalcogen bond: a sister noncovalent bond to halogen bond. J Phys Chem A 2009; 113:8132-5. [PMID: 19537765 DOI: 10.1021/jp904128b] [Citation(s) in RCA: 418] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A sister noncovalent bond to halogen bond, termed chalcogen bond, is defined in this article. By selecting the complexes H(2)CS...Cl(-), F(2)CS...Cl(-), OCS...Cl(-), and SCS...Cl(-) as models, the bond-length change, interaction energy, topological property of the electron charge density and its Laplacian, and the charge transfer of the chalcogen bond have been investigated in detail theoretically. It was found that the similar misshaped electron clouds of the chalcogen atom and the halogen atom result in the similar properties of the chalcogen bond and the halogen bond. Experimental results are in good agreement with the theoretical predictions.
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Affiliation(s)
- Weizhou Wang
- College of Chemistry and Chemical Engineering, Luoyang Normal University, Luoyang 471022, China
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27
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Harper K, Minofar B, Sierra-Hernandez MR, Casillas-Ituarte NN, Roeselova M, Allen HC. Surface Residence and Uptake of Methyl Chloride and Methyl Alcohol at the Air/Water Interface Studied by Vibrational Sum Frequency Spectroscopy and Molecular Dynamics. J Phys Chem A 2009; 113:2015-24. [DOI: 10.1021/jp808630v] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Kandice Harper
- Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, Institute of Physical Biology, University of South Bohemia, Zamek 136, Nove Hrady, Czech Republic, and Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, 16610 Prague 6, Czech Republic
| | - Babak Minofar
- Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, Institute of Physical Biology, University of South Bohemia, Zamek 136, Nove Hrady, Czech Republic, and Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, 16610 Prague 6, Czech Republic
| | - M. Roxana Sierra-Hernandez
- Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, Institute of Physical Biology, University of South Bohemia, Zamek 136, Nove Hrady, Czech Republic, and Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, 16610 Prague 6, Czech Republic
| | - Nadia N. Casillas-Ituarte
- Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, Institute of Physical Biology, University of South Bohemia, Zamek 136, Nove Hrady, Czech Republic, and Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, 16610 Prague 6, Czech Republic
| | - Martina Roeselova
- Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, Institute of Physical Biology, University of South Bohemia, Zamek 136, Nove Hrady, Czech Republic, and Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, 16610 Prague 6, Czech Republic
| | - Heather C. Allen
- Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, Institute of Physical Biology, University of South Bohemia, Zamek 136, Nove Hrady, Czech Republic, and Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, 16610 Prague 6, Czech Republic
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29
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Alkorta I, Blanco F, Solimannejad M, Elguero J. Competition of hydrogen bonds and halogen bonds in complexes of hypohalous acids with nitrogenated bases. J Phys Chem A 2008; 112:10856-63. [PMID: 18837495 DOI: 10.1021/jp806101t] [Citation(s) in RCA: 141] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A theoretical study of the complexes formed by hypohalous acids (HOX, X = F, Cl, Br, I, and At) with three nitrogenated bases (NH 3, N 2, and NCH) has been carried out by means of ab initio methods, up to MP2/aug-cc-pVTZ computational method. In general, two minima complexes are found, one with an OH...N hydrogen bond and the other one with a X...N halogen bond. While the first one is more stable for the smallest halogen derivatives, the two complexes present similar stabilities for the iodine case and the halogen-bonded structure is the most stable one for the hypoastatous acid complexes.
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Affiliation(s)
- Ibon Alkorta
- Instituto de Quimica Medica (CSIC), Juan de la Cierva, 3; 28006-Madrid, Spain.
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30
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Wang W, Hobza P. Origin of the X−Hal (Hal = Cl, Br) Bond-Length Change in the Halogen-Bonded Complexes. J Phys Chem A 2008; 112:4114-9. [PMID: 18345653 DOI: 10.1021/jp710992h] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Weizhou Wang
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center for Biomolecules and Complex Molecular Systems, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
| | - Pavel Hobza
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center for Biomolecules and Complex Molecular Systems, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
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Alkorta I, Solimannejad M, Provasi P, Elguero J. Theoretical study of complexes and fluoride cation transfer between N2F+ and electron donors. J Phys Chem A 2007; 111:7154-61. [PMID: 17602460 DOI: 10.1021/jp073112m] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A theoretical study of the complexes formed by the N2F cation (fluorodiazonium ion) and a series of small molecules containing nitrogen atoms have been carried out at the MP2 computational level. In addition, fluorine transfer has been studied. The electron density, NMR shielding and indirect coupling constants of the complexes have been evaluated. The covalent or halogen bonding characteristics of the N...F interactions observed in the complexes are defined by the interatomic distance. It has been determined that the limiting value is 1.6 A.
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Affiliation(s)
- Ibon Alkorta
- Instituto de Química Médica (CSIC), Juan de la Cierva 3, 28006-Madrid, Spain.
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Mora-Seró I, Anta JA, Dittrich T, Garcia-Belmonte G, Bisquert J. Continuous time random walk simulation of short-range electron transport in TiO2 layers compared with transient surface photovoltage measurements. J Photochem Photobiol A Chem 2006. [DOI: 10.1016/j.jphotochem.2006.04.029] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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33
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Lu Y, Zou J, Wang H, Yu Q, Zhang H, Jiang Y. Triangular halogen trimers. A DFT study of the structure, cooperativity, and vibrational properties. J Phys Chem A 2006; 109:11956-61. [PMID: 16366648 DOI: 10.1021/jp0547360] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Triangular halogen trimers (RX)3, where X = Br, I and R represents H, H3C, H2FC, HF2C, F3C, CH2=CH, CH[triple bond]C, and Ph, have been investigated using the density functional theory in the Perdew, Burke, and Ernzerhof method. We report herein the optimized geometries of the stable structures, their vibrational frequencies, and binding energies with the two- and three-body terms. All trimer structures possess a cyclic array of halogen atoms in the type II approach by virtue of the nonspherical atomic charge distribution around the halogens. The Br...Br interactions in trimers are very weak, whereas the I...I interactions in trimers are relatively stronger. While all bromine trimers and most of iodine trimers are predicted to be noncooperative, three of iodine trimers show weak cooperativity. The analysis of vibration modes reveals that all halogen trimers exhibit no especially remarkable frequency shifts. It is also shown that the electrostatic contribution plays a major role in the halogen...halogen interactions in halogen trimers. In contrast to bromine trimers, the relative contribution of charge-transfer component to the halogen...halogen interactions becomes more important for iodine trimers.
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Affiliation(s)
- Yunxiang Lu
- Department of Chemistry, Zhejiang University, Hangzhou, 310027, China
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Solimannejad M, Scheiner S. Weak hydrogen bonds in complexes pairing monohalomethanes with neutral formic acid. Chem Phys Lett 2006. [DOI: 10.1016/j.cplett.2006.04.052] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Solimannejad M, Scheiner S. Stabilities and Properties of Complexes Pairing Hydroperoxyl Radical with Monohalomethanes. J Phys Chem A 2006; 110:5948-51. [PMID: 16640394 DOI: 10.1021/jp060352d] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
UMP2/aug-cc-pvdz calculations are used to analyze the interaction between hydroperoxyl radical (HOO) and CH(3)X (X = F, Cl, Br). Two minima are located on the potential energy surface of each complex. The more strongly bound contains a OH...X bond, along with CH...O; only CH...O bonds occur in the less stable minimum. Binding energies of the dominant minimum lie in the range of 20-24 kJ/mol, with X = F the most strongly bound. Analysis of the perturbations of the covalent bond lengths within each subunit caused by complexation, coupled with vibrational frequencies and charge transfers, opens a window into the nature of the interactions.
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