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Scheiner S. Tetrel Bonding of the Carbenium Ion Forms a Pentacoordinate Carbon Atom. Chemphyschem 2024; 25:e202400240. [PMID: 38527952 DOI: 10.1002/cphc.202400240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 03/22/2024] [Accepted: 03/25/2024] [Indexed: 03/27/2024]
Abstract
As a flat trigonal species, the CR3 + carbenium ion contains a pair of deep π-holes above and below its molecular plane. In the case of CH3 + a first base will form a covalent bond with the central C, making the combined species tetrahedral. Approach of a second base to the opposite side results in a longer but rather strong noncovalent tetrel bond (TB). While CMe3 + can also form a similar asymmetric complex with a pair of bases, it also has the capacity to form a pair of nearly equivalent TBs, such that the resulting symmetric trigonal bipyramid configuration is only slightly higher in energy. When the three substituents on the central C are phenyl rings, the symmetric configuration with two TBs predominates. These tetrel bonds are quite strong, reaching up to 20 kcal/mol. Adding OPH2 or OCH substituents to the phenyl rings permits the formation of intramolecular C⋅⋅O TBs to the central C, very similar in many respects to the case where these TBs are intermolecular.
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Affiliation(s)
- Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, 84322-0300, Logan, Utah, USA
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2
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Scheiner S. Transition from covalent to noncovalent bonding between tetrel atoms. Phys Chem Chem Phys 2024; 26:15978-15986. [PMID: 38775057 DOI: 10.1039/d4cp01598c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2024]
Abstract
The strength and nature of the bonding between tetrel (T) atoms in R2T⋯TR2 is examined by quantum calculations. T atoms cover the range of Group 14 atoms from C to Pb, and substituents R include Cl, F, and NH2. Systems vary from electrically neutral to both positive and negative overall charged radicals. There is a steady weakening progression in T-T bond strength as the tetrel atom grows larger, transitioning smoothly from a strong covalent to a much weaker noncovalent bond for the larger T atoms. The latter have some of the characteristics of a ditetrel bond, but there are also significant deviations from a classic bond of this type. The T2Cl4- anions are more strongly bonded than the corresponding cations, which are in turn stronger than the neutrals.
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Affiliation(s)
- Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University Logan, Utah 84322-0300, USA.
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Michalczyk M, Zierkiewicz W, Scheiner S. Wolfium bonds in homodimers of MX 4Y (M = Mo, W; X = F, Cl, Br; Y = O, S, Se). Phys Chem Chem Phys 2024; 26:5836-5847. [PMID: 38299423 DOI: 10.1039/d3cp05867k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2024]
Abstract
The term "wolfium bond" has been recently introduced to describe the noncovalent attraction between an atom of group 6 and a nucleophile via a σ-hole binding site. Crystal structures commonly contain a motif wherein two MX4Y units are arranged in close proximity, where M represents either Mo or W, and X and Y refer to halogen and chalcogen atoms respectively. DFT calculations were thus applied to a wide range of homodimers of these molecules so as to assess their preferred arrangements, and to characterize the types of bonding that are present in each in a systematic manner. The most stable Dual-X configuration is symmetric and contains a pair of equivalent M⋯X bonds. The interaction energies range from -8 to -29 kcal mol-1, and are largest for X = F, Y = O, and M = W. The X electron donor is replaced by Y, and the two wolfium bonds are reduced to one, in the less stable Mono-Y structure, with interaction energies between -2 and -10 kcal mol-1. There is some question as to whether the weaker bonds of this type constitute true wolfium bonds.
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Affiliation(s)
- Mariusz Michalczyk
- 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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Scheiner S, Michalczyk M, Zierkiewicz W. Influence of Internal Angular Arrangement on Pnicogen Bond Strength. Inorg Chem 2023. [PMID: 38016913 DOI: 10.1021/acs.inorgchem.3c03141] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2023]
Abstract
The three Z-X covalent bonds of a ZX3 unit (Z = P, As, Sb, Bi) are normally arranged in a pyramidal structure. Quantum chemical calculations show that pnicogen bonds (ZBs) to the central Z are weakened if ZX3 is flattened, as in the opening of an umbrella. The partial closing of the umbrella has the opposite effect of substantially strengthening these ZBs, even amounting to a 2- or 3-fold magnification in certain cases. The strongest such bonds, wherein Sb and Bi are in a strained configuration within a ZO3CH model system, have interaction energies of 20 kcal/mol with an NH3 base. Most of these systems, whether flattened or more pyramidal, are capable of engaging in three ZBs simultaneously, despite a certain amount of negative cooperativity.
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Affiliation(s)
- Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322-0300, United States
| | - Mariusz Michalczyk
- 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
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Abstract
The properties of the bond between a N-ligand and a Lewis acid containing a σ-hole are studied by quantum chemical methods. Interactions considered include pnicogen bonds involving SbX5, PX5, and PX3, where X represents any of the halogen atoms F, Cl, Br, or I. Also studied are the tetrel bonds of PbX4 and SiX4, as well as the chalcogen bond involving TeOX4. Both NH3 and NCH are applied as two possible bases of differing potency. Some of the bonds are very strong with interaction energies easily exceeding 25 kcal/mol and with AIM bond critical point densities much higher than 0.04 au, suggesting their classification as coordinate covalent bonds. The pentavalent SbX5 and PX5 fall into this category when combined with NH3, as does TeOX4. Although the tetrel bonds involving PbX4 are only slightly weaker, they are probably better viewed as a strong noncovalent bond on the cusp of covalency. Changing the internal bonding of hypervalent SbX5 to the more conventional SbX3 weakens the interaction to a classical noncovalent pnicogen bond. Reducing the base nucleophilicity from NH3 to NCH weakens the bonds so that they are clearly noncovalent.
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Affiliation(s)
- Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322-0300, United States
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Amonov A, Scheiner S. Heavy pnicogen atoms as electron donors in sigma-hole bonds. Phys Chem Chem Phys 2023; 25:23530-23537. [PMID: 37656119 DOI: 10.1039/d3cp03479h] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
DFT calculations evaluate the strength of σ-hole bonds formed by ZH3 and ZMe3 (Z = N, P, As, Sb) acting as electron donor. Bond types considered include H-bond, halogen, chalcogen, pnicogen, and tetrel bond to perfluorinated Lewis acids FH, FBr, F2Se F3As, F4Ge, respectively, as well as their monofluorinated analogues. All of the Z atoms can engage in bonds of at least moderate strength, varying from 3 to more than 40 kcal mol-1. In most cases, N forms the strongest bonds, but the falloff from P to Sb is quite mild. However, this pattern is not characteristic of all cases, as for example in the halogen bonds, where the heavier Z atoms are comparable to, or even stronger than N. Most of the bonds are strengthened by replacing the three H atoms of ZH3 by methyl groups, better simulating the situation that would be generally encountered. Structural and NMR shielding data ought to facilitate the identification of these bonds within crystals or in solution.
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Affiliation(s)
- Akhtam Amonov
- Department of Optics and Spectroscopy Engineering Physics Institute, Samarkand State University, University blv. 15, Samarkand 140104, Uzbekistan
| | - Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University Logan, Utah 84322-0300, USA.
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Amonov A, Scheiner S. Competition between Binding to Various Sites of Substituted Imidazoliums. J Phys Chem A 2023. [PMID: 37490696 DOI: 10.1021/acs.jpca.3c04097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2023]
Abstract
The imidazolium cation has a number of different sites that can interact with a nucleophile. Adding a halogen atom (X) or a chalcogen (YH) group introduces the possibility of an NX···nuc halogen or NY···nuc chalcogen bond, which competes against the various H-bonds (NH and CH donors) as well as the lone pair···π interaction wherein the nucleophile lies above the plane of the cation. Substituted imidazoliums are paired with the NH3 base, and the various different complexes are evaluated by density functional theory (DFT) calculations. The strength of XB and YB increases quickly along with the size and polarizability of the X/Y atom, and this sort of bond is the strongest for the heavier Br, I, Se, and Te atoms, followed by the NH···N H-bond, but this order reverses for Cl and S. The various CH···N H-bonds are comparable to one another and to the lone pair···π bond, all with interaction energies of 10-13 kcal/mol, values which show very little dependence upon the substituent placed on the imidazolium.
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Affiliation(s)
- Akhtam Amonov
- Department of Optics and Spectroscopy, Engineering Physics Institute, Samarkand State University, University blv. 15, Samarkand 140104, Uzbekistan
| | - Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322-0300, United States
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Abstract
Quantum calculations study the potential of an intramolecular H-bond between the halogen atom (X) of a halobenzene and a substituent placed ortho to it, to amplify the ability of X to engage in a halogen bond (XB) with a Lewis base. H-bonding substituents NH2, CH2CH2OH, CH2OH, OH, and COOH were added to halobenzenes (X = Cl, Br, I). The amino group had little effect, but those containing OH increased the CX···N XB energy to a NH3 nucleophile by about 0.5 kcal/mol; the increment associated with COOH is larger, nearly 2 kcal/mol. These energy increments were approximately doubled if two such H-bonding substituents are present. Combining a pair of ortho COOH groups with an electron-withdrawing NO2 group in the para position has a particularly large effect, raising the XB energy by about 4 kcal/mol, which can amount to as much as a 4-fold magnification.
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Affiliation(s)
- Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322-0300, United States
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9
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Karir G, Lüttschwager NOB, Suhm MA. Phenylacetylene as a gas phase sliding balance for solvating alcohols. Phys Chem Chem Phys 2019; 21:7831-7840. [PMID: 30933202 DOI: 10.1039/c9cp00435a] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Phenylacetylene offers two similarly attractive π binding sites to OH containing solvent molecules, the phenyl ring and the acetylenic triple bond. By systematically varying the solvent molecule and by methylating aromatic or acetylenic CH groups, the docking preference can be controlled. It ranges from almost exclusive acetylene docking to predominant phenyl docking, depending on how electron density is deposited into the conjugated system and how large the London dispersion interaction is. FTIR spectroscopy of supersonic jet expansions is used to observe the competitive docking preferences in phenylacetylene and some of its methylated derivatives. A new data evaluation procedure that estimates band strength uncertainties based on a Monte Carlo approach is introduced. We test how well two density functionals (B3LYP-D3 and M06-2X) in combination with a def2-TZVP basis set are able to describe the docking switch. B3LYP-D3 is slightly biased towards acetylenic hydrogen bond docking and M06-2X is strongly biased towards phenyl hydrogen bond docking. More accurate theoretical predictions are invited and some previous experimental assignments are questioned.
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Affiliation(s)
- Ginny Karir
- Institut für Physikalische Chemie, Georg-August-Universität Göttingen, Tammannstraße 6, 37077 Göttingen, Germany.
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Karir G, Kumar G, Kar BP, Viswanathan KS. Multiple Hydrogen Bond Tethers for Grazing Formic Acid in Its Complexes with Phenylacetylene. J Phys Chem A 2018; 122:2046-2059. [DOI: 10.1021/acs.jpca.7b11428] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ginny Karir
- Department of Chemical Sciences, Indian Institute of Science Education and Research, Sector 81, Mohali 140306, Punjab India
| | - Gaurav Kumar
- Department of Chemical Sciences, Indian Institute of Science Education and Research, Sector 81, Mohali 140306, Punjab India
| | - Bishnu Prasad Kar
- Department of Chemical Sciences, Indian Institute of Science Education and Research, Sector 81, Mohali 140306, Punjab India
| | - K. S. Viswanathan
- Department of Chemical Sciences, Indian Institute of Science Education and Research, Sector 81, Mohali 140306, Punjab India
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11
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Karir G, Viswanathan KS. H−π Landscape of the Phenylacetylene–HCl System: Does This Provide the Gateway to the Markovnikov Addition? J Phys Chem A 2017; 121:5797-5808. [DOI: 10.1021/acs.jpca.7b04853] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ginny Karir
- Department of Chemical Sciences, Indian Institute of Science Education and Research, Sector 81, Mohali 140306, Punjab India
| | - K. S. Viswanathan
- Department of Chemical Sciences, Indian Institute of Science Education and Research, Sector 81, Mohali 140306, Punjab India
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12
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Saini J, Viswanathan KS. Discerning Near-Isoergic Isomers. A Matrix Isolation Infrared and ab Initio Study of the Propargyl Alcohol Dimers. J Phys Chem A 2017; 121:1448-1459. [DOI: 10.1021/acs.jpca.6b12702] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jyoti Saini
- Department of Chemical Sciences, Indian Institute of Science Education and Research, Mohali, Punjab 140306, India
| | - K. S. Viswanathan
- Department of Chemical Sciences, Indian Institute of Science Education and Research, Mohali, Punjab 140306, India
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13
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Scheiner S. Highly Selective Halide Receptors Based on Chalcogen, Pnicogen, and Tetrel Bonds. Chemistry 2016; 22:18850-18858. [PMID: 27740702 DOI: 10.1002/chem.201603891] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Indexed: 11/09/2022]
Abstract
The interactions of halides with a number of bipodal receptors were examined by quantum chemical methods. The receptors were based on a dithieno thiophene framework in which two S atoms can engage in a pair of chalcogen bonds with a halide. These two S atoms were replaced by P and As atoms to compare chalcogen with pnicogen bonding, and by Ge which engages in tetrel bonds with the receptor. Zero, one, and two O atoms were added to the thiophene S atom which is not directly involved in the interaction with the halides. Fluoride bound the most strongly, followed by Cl- , Br- , and I- , respectively. Replacing S by the pnicogen bonds of P strengthened the binding, as did moving down to As in the third row of the periodic table. A further large increment is associated with the switch to the tetrel bonds of Ge. Even though the thiophene S atom is remote from the binding site, each additional O atom added to it raises the binding energy, which can be quite large, as much as 63 kcal mol-1 for the Ge⋅⋅⋅F- interaction. The receptors have a pronounced selectivity for F- over the other halides, as high as 27 orders of magnitude. The data suggest that incorporation of tetrel atoms may lead to new and more powerful halide receptors.
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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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14
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Isaev AN. O–H···C hydrogen bond in the methane–water complex. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2016. [DOI: 10.1134/s0036024416100150] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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15
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Isaev AN. Intermolecular charge transfer as evidence for unusual O–H⋯C(sp3) hydrogen bond. COMPUT THEOR CHEM 2016. [DOI: 10.1016/j.comptc.2016.06.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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16
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Isaev AN. Hydrogen bonded С–H···Y (Y = O, S, Hal) molecular complexes: A natural bond orbital analysis. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2016. [DOI: 10.1134/s0036024416030183] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Pandey KK. Does hydrohalic acid HX (X = F, Cl) form true N-protonated twisted amide salts? Effects of anions on the ion-pair interactions and on the amide moiety in N-protonated tricyclic twisted amide salts. NEW J CHEM 2016. [DOI: 10.1039/c6nj01342b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The [BF4]− and [RSO3]− anions interact with N-protonated amide cations through N–H⋯F and N–H⋯O strong hydrogen bonds and hydrohalic acids form very weak N⋯H–X hydrogen bonds.
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Affiliation(s)
- Krishna K. Pandey
- School of Chemical Sciences
- Devi Ahilya University Indore
- Indore-452017
- India
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18
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Verma K, Dave K, Viswanathan KS. Hydrogen-Bonded Complexes of Phenylacetylene-Acetylene: Who is the Proton Donor? J Phys Chem A 2015; 119:12656-64. [PMID: 26643730 DOI: 10.1021/acs.jpca.5b08559] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Hydrogen-bonded complexes of C2H2 and phenylacetylene (PhAc) were studied using matrix isolation infrared spectroscopy and quantum chemical computations. Both C2H2 and PhAc, being potential proton donors, the question arises as to which of the two species would be the proton donor in the PhAc-C2H2 complex; a question that this work primarily addresses. The molecular structures, vibrational frequencies, and interaction energies of the PhAc-C2H2 complexes were calculated at the M06-2X and MP2 levels of theory, employing both 6-311++G(d,p) and aug-cc-pVDZ basis sets. At the M06-2X/aug-cc-pVDZ level, two nearly isoenergetic complexes (BSSE corrected) were indicated to be the global minima; one a C-H···π complex, where C2H2 served as a proton donor to the phenyl π-system in PhAc, and the other a C-H···π complex, where C2H2 served as a proton donor to the acetylene π-system in PhAc. Of the two, only the second complex was identified in the matrix, evidenced by a characteristic large shift in the ≡C-H stretch of C2H2. Experiments were also performed using PhAc deuterated at the acetylene hydrogen (PhAcD) to study the isotopic effects on the vibrational spectra of complexes. The isotopic studies further confirmed the structure of the complex trapped in the matrix, thereby presenting unambiguous evidence that C2H2 served as the proton donor to the acetylene π-system of PhAc. The theory of atoms-in-molecules (AIM), energy decomposition (EDA), and natural bond orbital (NBO) analysis were performed to understand the nature of the interactions involved in the complexes.
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Affiliation(s)
- Kanupriya Verma
- Department of Chemistry, Indian Institute of Science Education and Research , Sector 81, Mohali 140306, Punjab, India
| | - Kapil Dave
- Department of Chemistry, Indian Institute of Science Education and Research , Sector 81, Mohali 140306, Punjab, India
| | - K S Viswanathan
- Department of Chemistry, Indian Institute of Science Education and Research , Sector 81, Mohali 140306, Punjab, India
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Pandey KK. Structure and bonding analysis of germanones [(Eind) 2 Ge O], [((Tbt))(Tip)Ge O] and [R 2 Ge O] (R = Me, Ph): Significance of the dispersion interactions. COMPUT THEOR CHEM 2015. [DOI: 10.1016/j.comptc.2015.09.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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20
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Pandey KK. Theoretical insights into structure, bonding, reactivity and importance of ion-pair interactions in Kirby's tetrafluoroboric acid salts of twisted amides. RSC Adv 2015. [DOI: 10.1039/c5ra22792e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The hydrolysis of amide 1 is more exothermic and is more favorable than amides 2 and 3 with bridgehead methyl.
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Affiliation(s)
- Krishna K. Pandey
- School of Chemical Sciences
- D. A. University Indore
- Indore 452 017
- India
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21
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Horowitz S, Adhikari U, Dirk LMA, Del Rizzo PA, Mehl RA, Houtz RL, Al-Hashimi HM, Scheiner S, Trievel RC. Manipulating unconventional CH-based hydrogen bonding in a methyltransferase via noncanonical amino acid mutagenesis. ACS Chem Biol 2014; 9:1692-7. [PMID: 24914947 DOI: 10.1021/cb5001185] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Recent studies have demonstrated that the active sites of S-adenosylmethionine (AdoMet)-dependent methyltransferases form strong carbon-oxygen (CH···O) hydrogen bonds with the substrate's sulfonium group that are important in AdoMet binding and catalysis. To probe these interactions, we substituted the noncanonical amino acid p-aminophenylalanine (pAF) for the active site tyrosine in the lysine methyltransferase SET7/9, which forms multiple CH···O hydrogen bonds to AdoMet and is invariant in SET domain enzymes. Using quantum chemistry calculations to predict the mutation's effects, coupled with biochemical and structural studies, we observed that pAF forms a strong CH···N hydrogen bond to AdoMet that is offset by an energetically unfavorable amine group rotamer within the SET7/9 active site that hinders AdoMet binding and activity. Together, these results illustrate that the invariant tyrosine in SET domain methyltransferases functions as an essential hydrogen bonding hub and cannot be readily substituted by residues bearing other hydrogen bond acceptors.
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Affiliation(s)
- Scott Horowitz
- Howard Hughes Medical Institute, Ann Arbor, Michigan 48109, United States
| | - Upendra Adhikari
- Department
of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322, United States
| | - Lynnette M. A. Dirk
- Department
of Horticulture, University of Kentucky, Lexington, Kentucky 40546, United States
| | | | - Ryan A. Mehl
- Department
of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, United States
| | - Robert L. Houtz
- Department
of Horticulture, University of Kentucky, Lexington, Kentucky 40546, United States
| | | | - Steve Scheiner
- Department
of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322, United States
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22
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Adhikari U, Scheiner S. First steps in growth of a polypeptide toward β-sheet structure. J Phys Chem B 2013; 117:11575-83. [PMID: 24028425 DOI: 10.1021/jp406326h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The full conformational energy surface is examined for a molecule in which a dipeptide is attached to the same spacer group as another peptide chain, so as to model the seminal steps of β-sheet formation. This surface is compared with the geometrical preferences of the isolated dipeptide to extract the perturbations induced by interactions with the second peptide strand. These interpeptide interactions remove any tendency of the dipeptide to form a C5 ring structure, one of its two normally stable geometries. A C7 structure, the preferred conformation of the isolated dipeptide, remains as the global minimum in the full molecule. However, the stability of this structure is highly dependent upon interpeptide H-bonds with the second chain. The latter forces include not only the usual NH···O interaction, but also a pair of CH···O H-bonds. The secondary minimum is also of C7 type and likewise depends in part upon CH···O H-bonds for its stability. The latter interactions also play a part in the tertiary minimum. A two-strand β-sheet structure is not yet in evidence for this small model system, requiring additional peptide units to be added to each chain.
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Affiliation(s)
- Upendra Adhikari
- Department of Chemistry and Biochemistry, Utah State University , Logan, Utah 84322-0300, United States
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23
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Sundararajan K, Ramanathan N, Viswanathan K, Vidya K, Jemmis ED. Complexes of acetylene–fluoroform: A matrix isolation and computational study. J Mol Struct 2013. [DOI: 10.1016/j.molstruc.2013.05.069] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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24
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Adhikari U, Scheiner S. Magnitude and Mechanism of Charge Enhancement of CH··O Hydrogen Bonds. J Phys Chem A 2013; 117:10551-62. [DOI: 10.1021/jp4081788] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Upendra Adhikari
- 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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Ito F. Matrix-isolation infrared studies of 1:1 molecular complexes containing chloroform (CHCl3) and Lewis bases: Seamless transition from blue-shifted to red-shifted hydrogen bonds. J Chem Phys 2012; 137:014505. [DOI: 10.1063/1.4730909] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Minenkov Y, Singstad Å, Occhipinti G, Jensen VR. The accuracy of DFT-optimized geometries of functional transition metal compounds: a validation study of catalysts for olefin metathesis and other reactions in the homogeneous phase. Dalton Trans 2012; 41:5526-41. [DOI: 10.1039/c2dt12232d] [Citation(s) in RCA: 358] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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Marom N, Tkatchenko A, Rossi M, Gobre VV, Hod O, Scheffler M, Kronik L. Dispersion Interactions with Density-Functional Theory: Benchmarking Semiempirical and Interatomic Pairwise Corrected Density Functionals. J Chem Theory Comput 2011; 7:3944-51. [PMID: 26598340 DOI: 10.1021/ct2005616] [Citation(s) in RCA: 186] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We present a comparative assessment of the accuracy of two different approaches for evaluating dispersion interactions: interatomic pairwise corrections and semiempirical meta-generalized-gradient-approximation (meta-GGA)-based functionals. This is achieved by employing conventional (semi)local and (screened-)hybrid functionals, as well as semiempirical hybrid and nonhybrid meta-GGA functionals of the M06 family, with and without interatomic pairwise Tkatchenko-Scheffler corrections. All of those are tested against the benchmark S22 set of weakly bound systems, a representative larger molecular complex (dimer of NiPc molecules), and a representative dispersively bound solid (hexagonal boron nitride). For the S22 database, we also compare our results with those obtained from the pairwise correction of Grimme (DFT-D3) and nonlocal Langreth-Lundqvist functionals (vdW-DF1 and vdW-DF2). We find that the semiempirical kinetic-energy-density dependence introduced in the M06 functionals mimics some of the nonlocal correlation needed to describe dispersion. However, long-range contributions are still missing. Pair-wise interatomic corrections, applied to conventional semilocal or hybrid functionals, or to M06 functionals, provide for a satisfactory level of accuracy irrespectively of the underlying functional. Specifically, screened-hybrid functionals such as the Heyd-Scuseria-Ernzerhof (HSE) approach reduce self-interaction errors in systems possessing both localized and delocalized orbitals and can be applied to both finite and extended systems. Therefore, they serve as a useful underlying functional for dispersion corrections.
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Affiliation(s)
- Noa Marom
- Department of Materials and Interfaces, Weizmann Institute of Science , Rehovoth 76100, Israel.,Center for Computational Materials, Institute for Computational Engineering and Sciences, University of Texas at Austin , Austin, Texas 78712, United States
| | - Alexandre Tkatchenko
- Fritz-Haber-Institut der Max-Planck-Gesellschaft , Faradayweg 4-6, 14195 Berlin, Germany
| | - Mariana Rossi
- Fritz-Haber-Institut der Max-Planck-Gesellschaft , Faradayweg 4-6, 14195 Berlin, Germany
| | - Vivekanand V Gobre
- Fritz-Haber-Institut der Max-Planck-Gesellschaft , Faradayweg 4-6, 14195 Berlin, Germany
| | - Oded Hod
- School of Chemistry, The Sackler Faculty of Exact Sciences, Tel Aviv University , Tel Aviv 69978, Israel
| | - Matthias Scheffler
- Fritz-Haber-Institut der Max-Planck-Gesellschaft , Faradayweg 4-6, 14195 Berlin, Germany
| | - Leeor Kronik
- Department of Materials and Interfaces, Weizmann Institute of Science , Rehovoth 76100, Israel
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Obenchain DA, Bills BJ, Christenholz CL, Elmuti LF, Peebles RA, Peebles SA, Neill JL, Steber AL. C–H···π Interactions in the CHBrF2···HCCH Weakly Bound Dimer. J Phys Chem A 2011; 115:12228-34. [DOI: 10.1021/jp208603m] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Daniel A. Obenchain
- Department of Chemistry, Eastern Illinois University, 600 Lincoln Avenue, Charleston, Illinois 61920, United States
| | - Brandon J. Bills
- Department of Chemistry, Eastern Illinois University, 600 Lincoln Avenue, Charleston, Illinois 61920, United States
| | - Cori L. Christenholz
- Department of Chemistry, Eastern Illinois University, 600 Lincoln Avenue, Charleston, Illinois 61920, United States
| | - Lena F. Elmuti
- Department of Chemistry, Eastern Illinois University, 600 Lincoln Avenue, Charleston, Illinois 61920, United States
| | - Rebecca A. Peebles
- Department of Chemistry, Eastern Illinois University, 600 Lincoln Avenue, Charleston, Illinois 61920, United States
| | - Sean A. Peebles
- Department of Chemistry, Eastern Illinois University, 600 Lincoln Avenue, Charleston, Illinois 61920, United States
| | - Justin L. Neill
- Department of Chemistry, University of Virginia, McCormick Road, PO Box 400319, Charlottesville, Virginia 22904, United States
| | - Amanda L. Steber
- Department of Chemistry, University of Virginia, McCormick Road, PO Box 400319, Charlottesville, Virginia 22904, United States
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Elmuti LF, Peebles RA, Peebles SA, Steber AL, Neill JL, Pate BH. Observation of a double C–H⋯π interaction in the CH2ClF⋯HCCH weakly bound complex. Phys Chem Chem Phys 2011; 13:14043-9. [DOI: 10.1039/c1cp20684b] [Citation(s) in RCA: 9] [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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