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Tupikina EY, Titova AA, Kaplanskiy MV, Chakalov ER, Kostin MA, Tolstoy PM. Estimations of OH·N hydrogen bond length from positions and intensities of IR bands. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 275:121172. [PMID: 35366525 DOI: 10.1016/j.saa.2022.121172] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 03/02/2022] [Accepted: 03/15/2022] [Indexed: 06/14/2023]
Abstract
In this computational work applicability of IR spectral parameters for evaluations of OH···N hydrogen bond length is discussed. For a set of 124 complexes with OH···N hydrogen bond formed by combinations of methanol/acetic acid and pyridine (and their fluorine substituted versions) geometries, energies and IR parameters were calculated at MP2/def2-TZVP level of theory. For a number of IR parameters (the shift of proton donor group stretching vibration Δνs, increase of its intensity I, the low-frequency hydrogen bond stretching vibration νσ, bending in-plane δ and out-of-plane γ vibrations) equations linking them with interatomic distances are proposed, the robustness and accuracy of such equations are discussed. The enthalpy of OH···N hydrogen bond formation ΔH was also linked with electron density parameters in (3; -1) critical point.
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Affiliation(s)
- E Yu Tupikina
- Institute of Chemistry, St. Petersburg State University, St. Petersburg, Russia.
| | - A A Titova
- Institute of Chemistry, St. Petersburg State University, St. Petersburg, Russia
| | - M V Kaplanskiy
- Institute of Chemistry, St. Petersburg State University, St. Petersburg, Russia
| | - E R Chakalov
- Institute of Chemistry, St. Petersburg State University, St. Petersburg, Russia
| | - M A Kostin
- Institute of Chemistry, St. Petersburg State University, St. Petersburg, Russia; Department of Physics, St. Petersburg State University, St. Petersburg, Russia
| | - P M Tolstoy
- Institute of Chemistry, St. Petersburg State University, St. Petersburg, Russia.
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2
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Simultaneous Estimation of Two Coupled Hydrogen Bond Geometries from Pairs of Entangled NMR Parameters: The Test Case of 4-Hydroxypyridine Anion. Molecules 2022; 27:molecules27123923. [PMID: 35745047 PMCID: PMC9229270 DOI: 10.3390/molecules27123923] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 06/15/2022] [Accepted: 06/16/2022] [Indexed: 02/05/2023] Open
Abstract
The computational method for estimating the geometry of two coupled hydrogen bonds with geometries close to linear using a pair of spectral NMR parameters was proposed. The method was developed based on the quantum-chemical investigation of 61 complexes with two hydrogen bonds formed by oxygen and nitrogen atoms of the 4-hydroxypyridine anion with OH groups of substituted methanols. The main idea of the method is as follows: from the NMR chemical shifts of nuclei of atoms forming the 4-hydroxylpyridine anion, we select such pairs, whose values can be used for simultaneous determination of the geometry of two hydrogen bonds, despite the fact that every NMR parameter is sensitive to the geometry of each of the hydrogen bonds. For these parameters, two-dimensional maps of dependencies of NMR chemical shifts on interatomic distances in two hydrogen bonds were constructed. It is shown that, in addition to chemical shifts of the nitrogen atom and quaternary carbon, which are experimentally difficult to obtain, chemical shifts of the carbons and protons of the CH groups can be used. The performance of the proposed method was evaluated computationally as well on three additional complexes with substituted alcohols. It was found that, for all considered cases, hydrogen bond geometries estimated using two-dimensional correlations differed from those directly calculated by quantum-chemical methods by not more than 0.04 Å.
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3
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Hansen PE, Saeed BA, Rutu RS, Kupka T. One-bond 1 J( 15 N,H) coupling constants at sp 2 -hybridized nitrogen of Schiff bases, enaminones and similar compounds: A theoretical study. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2020; 58:750-762. [PMID: 32415997 DOI: 10.1002/mrc.5052] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 05/07/2020] [Accepted: 05/11/2020] [Indexed: 06/11/2023]
Abstract
1 J(15 N,H) coupling constants for enaminones and NH-forms of intramolecularly hydrogen-bonded Schiff bases as model compounds for sp2 -hybridized nitrogen atoms are evaluated using density functional theory (DFT) to find the optimal functionals and basis sets. Ammonia is used as a test molecule and its one-bond coupling constant is compared with experiment. A methylamine Schiff base of a truncated molecule of gossypol is used for checking the performance of selected B3LYP, O3LYP, PBE, BHandH, and APFD density functionals and standard, modified, and dedicated basis sets for coupling constants. Both in vacuum and in chloroform, modeled by the simple continuum model of solvent, the modified basis sets predict significantly better the 1 J(15 N,H) value in ammonia and in the methylamine Schiff base of a truncated molecule of gossypol than the standard basis sets. This procure is then used on a broad set of intramolecularly hydrogen-bonded molecules, and a good correlation between calculated and experimental one-bond NH coupling constants is obtained. The 1 J(15 N,H) couplings are slightly overestimated. The calculated data show for hydrogen-bonded NH interatomic distances that the calculated values depend on the NH bond lengths. The shorter the bond lengths, the larger the 1 J(15 N,H). A useful correlation between 1 J(15 N,H) and NH bond length is derived that enables realistic predictions of one-bond NH coupling constants. The calculations reproduce experimentally observed trends for the studied molecules.
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Affiliation(s)
- Poul Erik Hansen
- Department of Science and Environment, Roskilde University, Roskilde, Denmark
| | - Bahjat A Saeed
- Department of Chemistry, College of Education for Pure Sciences, University of Basrah, Iraq
| | - Rita S Rutu
- Department of Pharmaceutical Chemistry, College of Pharmacy, University of Basrah, Iraq
| | - Teobald Kupka
- Faculty of Chemistry, University of Opole, Opole, Poland
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4
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Petrova M, Muhamadejev R, Vigante B, Duburs G, Liepinsh E. Intramolecular hydrogen bonds in 1,4-dihydropyridine derivatives. ROYAL SOCIETY OPEN SCIENCE 2018; 5:180088. [PMID: 30110409 PMCID: PMC6030305 DOI: 10.1098/rsos.180088] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 05/02/2018] [Indexed: 05/24/2023]
Abstract
1,4-Dihydropyridine (1,4-DHP) derivatives have been synthesized and characterized by 1H, 13C, 15N nuclear magnetic resonance (NMR) spectroscopy, secondary proton/deuterium 13C isotope shifts, variable temperature 1H NMR experiments and quantum-chemical calculation. The intramolecular hydrogen bonds NH⋯O=C and CH⋯O=C in these compounds were established by NMR and quantum-chemical studies The downfield shift of the NH proton, accompanied by the upfield shift of the 15N nuclear magnetic resonance signals, the shift to the higher wavenumbers of the NH stretching vibration in the infrared spectra and the increase of the 1J(15N,1H) values may indicate the shortening of the N-H bond length upon intramolecular NH⋯O=C hydrogen bond formation.
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Affiliation(s)
- M. Petrova
- Latvian Institute of Organic Synthesis, Aizkraukles 21 Street, Riga 1006, Latvia
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5
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Preimesberger M, Majumdar A, Rice SL, Que L, Lecomte JTJ. Helix-Capping Histidines: Diversity of N-H···N Hydrogen Bond Strength Revealed by (2h)JNN Scalar Couplings. Biochemistry 2015; 54:6896-908. [PMID: 26523621 PMCID: PMC4660981 DOI: 10.1021/acs.biochem.5b01002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Revised: 10/31/2015] [Indexed: 11/29/2022]
Abstract
In addition to its well-known roles as an electrophile and general acid, the side chain of histidine often serves as a hydrogen bond (H-bond) acceptor. These H-bonds provide a convenient pH-dependent switch for local structure and functional motifs. In hundreds of instances, a histidine caps the N-terminus of α- and 310-helices by forming a backbone NH···Nδ1 H-bond. To characterize the resilience and dynamics of the histidine cap, we measured the trans H-bond scalar coupling constant, (2h)JNN, in several forms of Group 1 truncated hemoglobins and cytochrome b5. The set of 19 measured (2h)JNN values were between 4.0 and 5.4 Hz, generally smaller than in nucleic acids (~6-10 Hz) and indicative of longer, weaker bonds in the studied proteins. A positive linear correlation between (2h)JNN and the difference in imidazole ring (15)N chemical shift (Δ(15)N = |δ(15)Nδ1 - δ(15)Nε2|) was found to be consistent with variable H-bond length and variable cap population related to the ionization of histidine in the capping and noncapping states. The relative ease of (2h)JNN detection suggests that this parameter can become part of the standard arsenal for describing histidines in helix caps and other key structural and catalytic elements involving NH···N H-bonds. The combined nucleic acid and protein data extend the utility of (2h)JNN as a sensitive marker of local structural, dynamic, and thermodynamic properties in biomolecules.
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Affiliation(s)
- Matthew
R. Preimesberger
- T.
C. Jenkins Department of Biophysics, Johns
Hopkins University, Baltimore, Maryland 21218, United States
| | - Ananya Majumdar
- Biomolecular
NMR Center, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Selena L. Rice
- T.
C. Jenkins Department of Biophysics, Johns
Hopkins University, Baltimore, Maryland 21218, United States
| | - Lauren Que
- T.
C. Jenkins Department of Biophysics, Johns
Hopkins University, Baltimore, Maryland 21218, United States
| | - Juliette T. J. Lecomte
- T.
C. Jenkins Department of Biophysics, Johns
Hopkins University, Baltimore, Maryland 21218, United States
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6
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Gurinov AA, Lesnichin SB, Limbach HH, Shenderovich IG. How short is the strongest hydrogen bond in the proton-bound homodimers of pyridine derivatives? J Phys Chem A 2014; 118:10804-12. [PMID: 25327551 DOI: 10.1021/jp5082033] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Hydrogen bond geometries in the proton-bound homodimers of ortho-unsubstituted and ortho-methylsubstituted pyridine derivatives in aprotic polar solution were estimated using experimental NMR data. Within the series of homodimers studied the hydrogen bond lengths depend on the proton affinity of pyridines and--at least for the ortho-methylsubstituted pyridines--on the pKa of the conjugate acids in an approximately quadratic manner. The shortest possible hydrogen bond in the homodimers of ortho-unsubstituted pyridines is characterized by the N···N distance of 2.613 Å. Steric repulsion between the methyl groups of the ortho-methylsubstituted pyridines becomes operative at an N···N distance of ∼2.7 Å and limits the closest approach to 2.665 Å.
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Affiliation(s)
- Andrey A Gurinov
- Institute of Chemistry and Biochemistry, Free University Berlin , Takustrasse 3, 14195 Berlin, Germany
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7
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Rusakov YY, Krivdin LB. Modern quantum chemical methods for calculating spin–spin coupling constants: theoretical basis and structural applications in chemistry. RUSSIAN CHEMICAL REVIEWS 2013. [DOI: 10.1070/rc2013v082n02abeh004350] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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8
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Melikova S, Rutkowski K, Gurinov A, Denisov G, Rospenk M, Shenderovich I. FTIR study of the hydrogen bond symmetry in protonated homodimers of pyridine and collidine in solution. J Mol Struct 2012. [DOI: 10.1016/j.molstruc.2011.12.027] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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9
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Kong S, Borissova AO, Lesnichin SB, Hartl M, Daemen LL, Eckert J, Antipin MY, Shenderovich IG. Geometry and spectral properties of the protonated homodimer of pyridine in the liquid and solid states. A combined NMR, X-ray diffraction and inelastic neutron scattering study. J Phys Chem A 2011; 115:8041-8. [PMID: 21644583 DOI: 10.1021/jp203543g] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The structure and spectral signatures of the protonated homodimer of pyridine in its complex with a poorly coordinating anion have been studied in solution in CDF(3)/CDClF(2) down to 120 K and in a single crystal. In both phases, the hydrogen bond is asymmetric. In the solution, the proton is involved in a fast reversible transfer that determines the multiplicity of NMR signals and the sign of the primary H/D isotope effect of --0.95 ppm. The proton resonates at 21.73 ppm that is above any value reported in the past and is indicative of a very short hydrogen bond. By combining X-ray diffraction analysis with model computations, the position of the proton in the crystal has been defined as d(N-H) = 1.123 Å and d(H···N) = 1.532 Å. The same distances have been estimated using a (15)N NMR correlation. The frequency of the protonic out-of-plane bending mode is 822 cm(-1) in agreement with Novak's correlation.
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Affiliation(s)
- S Kong
- Institut für Chemie und Biochemie, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany
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10
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Han LJ. Redetermination of ( E)- N, N′-bis(4-bromophenyl)formamidine. Acta Crystallogr Sect E Struct Rep Online 2011; 67:o1159. [PMID: 21754467 PMCID: PMC3089148 DOI: 10.1107/s1600536811013419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2011] [Accepted: 04/10/2011] [Indexed: 11/28/2022]
Abstract
In comprison with the previous structural study [Anulewicz et al. (1991 ▶). Pol. J. Chem.65, 465–471], for which only the coordinates of all non-H atoms and of some H atoms were reported, the current redetermination of the title compound, C13H10Br2N2, additionally reports anisotropic displacement parameters for all non-H atoms and the coordinates of all H atoms, accompanied by higher accuracy of the geometric parameters. Two independent half-molecules are present in the asymmetric unit, which are completed by a twofold rotation axis as symmetry element. In the crystal, intermolecular N—H⋯N hydrogen bonds link the molecules into dimers. Linear chains parallel to [102] are formed by intermolecular Br⋯Br interactions of 3.4328 (7) Å between two Br atoms of adjacent molecules. The dihedral angles between the benzene rings are 50.05 (15) and 75.61 (11)° in the two independent molecules. Owing to the twofold symmetry of the molecules, H atoms attached to the N atoms are only half-occupied, leading to them being disordered over two positions of equal occupancy.
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11
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Afonin AV, Ushakov IA, Vashchenko AV, Kondrashov EV, Rulev AY. GIAO, DFT, AIM and NBO analysis of the N-H...O intramolecular hydrogen-bond influence on the 1J(N,H) coupling constant in push-pull diaminoenones. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2010; 48:661-670. [PMID: 20661903 DOI: 10.1002/mrc.2643] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
In the series of diaminoenones, large high-frequency shifts of the (1)H NMR of the N-H group in the cis-position relative to the carbonyl group suggests strong N-H...O intramolecular hydrogen bonding comprising a six-membered chelate ring. The N-H...O hydrogen bond causes an increase of the (1)J(N,H) coupling constant by 2-4 Hz and high-frequency shift of the (15)N signal by 9-10 ppm despite of the lengthening of the relevant N-H bond. These experimental trends are substantiated by gauge-independent atomic orbital and density functional theory calculations of the shielding and coupling constants in the 3,3-bis(isopropylamino)-1-(aryl)prop-2-en-1-one (12) for conformations with the Z- and E-orientations of the carbonyl group relative to the N-H group. The effects of the N-H...O hydrogen-bond on the NMR parameters are analyzed with the atoms-in-molecules (AIM) and natural bond orbital (NBO) methods. The AIM method indicates a weakening of the N-H...O hydrogen bond as compared with that of 1,1-di(pyrrol-2-yl)-2-formylethene (13) where N-H...O hydrogen bridge establishes a seven-membered chelate ring, and the corresponding (1)J(N,H) coupling constant decreases. The NBO method reveals that the LP(O) --> sigma*(N-H) hyperconjugative interaction is weakened on going from the six-membered chelate ring to the seven-membered one due to a more bent hydrogen bond in the former case. A dominating effect of the N-H bond rehybridization, owing to an electrostatic term in the hydrogen bonding, seems to provide an increase of the (1)J(N,H) value as a consequence of the N-H...O hydrogen bonding in the studied diaminoenones.
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12
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Afonin AV, Ushakov IA, Pavlov DV, Ivanov AV, Mikhaleva AI. Study of conformations and hydrogen bonds in the configurational isomers of pyrrole-2-carbaldehyde oxime by 1H, 13C and 15N NMR spectroscopy combined with MP2 and DFT calculations and NBO analysis. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2010; 48:685-692. [PMID: 20623827 DOI: 10.1002/mrc.2650] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The (1)H, (13)C and (15)N NMR studies have shown that the E and Z isomers of pyrrole-2-carbaldehyde oxime adopt preferable conformation with the syn orientation of the oxime group with respect to the pyrrole ring. The syn conformation of E and Z isomers of pyrrole-2-carbaldehyde oxime is stabilized by the N-H...N and N-H...O intramolecular hydrogen bonds, respectively. The N-H...N hydrogen bond in the E isomer causes the high-frequency shift of the bridge proton signal by about 1 ppm and increase the (1)J(N, H) coupling by approximately 3 Hz. The bridge proton shows further deshielding and higher increase of the (1)J(N, H) coupling constant due to the strengthening of the N-H...O hydrogen bond in the Z isomer. The MP2 calculations indicate that the syn conformation of E and Z isomers is by approximately 3.5 kcal/mol energetically less favorable than the anti conformation. The calculations of (1)H shielding and (1)J(N, H) coupling in the syn and anti conformations allow the contribution to these constants from the N-H...N and N-H...O hydrogen bondings to be estimated. The NBO analysis suggests that the N-H...N hydrogen bond in the E isomer is a pure electrostatic interaction while the charge transfer from the oxygen lone pair to the antibonding orbital of the N-H bond through the N-H...O hydrogen bond occurs in the Z isomer.
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Affiliation(s)
- Andrei V Afonin
- Institute of Chemistry, Siberian Branch of the Russian Academy of Science, Favorski St 1, 664033 Irkutsk, Russia
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13
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14
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Del Bene JE, Alkorta I, Elguero J. Do corresponding coupling constants in hydrogen-bonded homo- and hetero-chiral dimers differ? CAN J CHEM 2010. [DOI: 10.1139/v09-177] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Ab initio equation-of-motion coupled cluster singles and doubles (EOM–CCSD) calculations have been carried out to evaluate spin–spin coupling constants in six pairs of homo- and hetero-chiral dimers: (HOOH)2, (H2NNH2)2, (FOOH)2, (FHNNH2)2, (HOOOH)2, and (FOOOH)2. Corresponding spin–spin coupling constants in these isomeric pairs of C2 and Ci symmetry may differ, but these differences are small and may not be detectable experimentally. For the complexes with O1–H···O and O1–H···F hydrogen bonds, 1J(O1–H) has a larger absolute value in the C2 isomer. For the same set of complexes, 1J(O1–O2) has a larger absolute value in the Ci isomer. No distinguishable patterns could be discerned in the remaining spin–spin coupling constants in the C2 and Ci isomers of these complexes, nor in complexes with N–H···N hydrogen bonds.
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Affiliation(s)
- Janet E. Del Bene
- Department of Chemistry, Youngstown State University, Youngstown, Ohio 44555, USA
- Instituto de Química Médica, CSIC (Consejo Superior de Investigaciones Científicas), Juan de la Cierva, 3, E-28006 Madrid, Spain
| | - Ibon Alkorta
- Department of Chemistry, Youngstown State University, Youngstown, Ohio 44555, USA
- Instituto de Química Médica, CSIC (Consejo Superior de Investigaciones Científicas), Juan de la Cierva, 3, E-28006 Madrid, Spain
| | - José Elguero
- Department of Chemistry, Youngstown State University, Youngstown, Ohio 44555, USA
- Instituto de Química Médica, CSIC (Consejo Superior de Investigaciones Científicas), Juan de la Cierva, 3, E-28006 Madrid, Spain
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15
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Afonin AV, Vashchenko AV. Theoretical study of bifurcated hydrogen bonding effects on the 1J(N,H), 1hJ(N,H), 2hJ(N,N) couplings and 1H, 15N shieldings in model pyrroles. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2010; 48:309-317. [PMID: 20198609 DOI: 10.1002/mrc.2579] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
According to the density functional theory calculations, the X...H...N (X=N, O) intramolecular bifurcated (three-centered) hydrogen bond with one hydrogen donor and two hydrogen acceptors causes a significant decrease of the (1h)J(N,H) and (2h)J(N,N) coupling constants across the N-H...N hydrogen bond and an increase of the (1)J(N,H) coupling constant across the N-H covalent bond in the 2,5-disubstituted pyrroles. This occurs due to a weakening of the N-H...N hydrogen bridge resulting in a lengthening of the N...H distance and a decrease of the hydrogen bond angle at the bifurcated hydrogen bond formation. The gauge-independent atomic orbital calculations of the shielding constants suggest that a weakening of the N-H...N hydrogen bridge in case of the three-centered hydrogen bond yields a shielding of the bridge proton and deshielding of the acceptor nitrogen atom. The atoms-in-molecules analysis shows that an attenuation of the (1h)J(N,H) and (2h)J(N,N) couplings in the compounds with bifurcated hydrogen bond is connected with a decrease of the electron density rho(H...N) at the hydrogen bond critical point and Laplacian of this electron density nabla(2)rho(H...N). The natural bond orbital analysis suggests that the additional N-H...X interaction partly inhibits the charge transfer from the nitrogen lone pair to the sigma*(N-H) antibonding orbital across hydrogen bond weakening of the (1h)J(N,H) and (2h)J(N,N) trans-hydrogen bond couplings through Fermi-contact mechanism. An increase of the nitrogen s-character percentage of the N-H bond in consequence of the bifurcated hydrogen bonding leads to an increase of the (1)J(N,H) coupling constant across the N-H covalent bond and deshielding of the hydrogen donor nitrogen atom.
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Affiliation(s)
- Andrei V Afonin
- Institute of Chemistry, Siberian Branch of the Russian Academy of Science, Favorski St. 1, 664033 Irkutsk, Russia.
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16
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Pietrzak M, Wehling J, Kong S, Tolstoy P, Shenderovich I, López C, Claramunt RM, Elguero J, Denisov G, Limbach HH. Symmetrization of Cationic Hydrogen Bridges of Protonated Sponges Induced by Solvent and Counteranion Interactions as Revealed by NMR Spectroscopy. Chemistry 2010; 16:1679-90. [DOI: 10.1002/chem.200902259] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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17
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Del Bene JE, Alkorta I, Elguero J. Characterizing Complexes with F−Li+−F Lithium Bonds: Structures, Binding Energies, and Spin−Spin Coupling Constants. J Phys Chem A 2009; 113:8359-65. [DOI: 10.1021/jp9020917] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Janet E. Del Bene
- Department of Chemistry, Youngstown State University, Youngstown, Ohio 44555, and Instituto de Química Médica, CSIC, Juan de la Cierva, 3, E-28006 Madrid, Spain
| | - Ibon Alkorta
- Department of Chemistry, Youngstown State University, Youngstown, Ohio 44555, and Instituto de Química Médica, CSIC, Juan de la Cierva, 3, E-28006 Madrid, Spain
| | - José Elguero
- Department of Chemistry, Youngstown State University, Youngstown, Ohio 44555, and Instituto de Química Médica, CSIC, Juan de la Cierva, 3, E-28006 Madrid, Spain
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18
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Alkorta I, Blanco F, Elguero J. A theoretical structural analysis of the factors that affect (1)J(NH), (1h)J(NH) and (2h)J(NN) in N-H...N hydrogen-bonded complexes. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2009; 47:249-256. [PMID: 19097158 DOI: 10.1002/mrc.2382] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Calculations of (1)J(NH), (1h)J(NH) and (2h)J(NN) spin-spin coupling constants of 27 complexes presenting N-H...N hydrogen bonds have allowed to analyze these through hydrogen-bond coupling as a function of the hybridization of both nitrogen atoms and the charge (+1, 0, - 1) of the complex. The main conclusions are that the hybridization of N atom of the hydrogen bond donor is much more important than that of the hydrogen bond acceptor. Positive and negative charges (cationic and anionic complexes) exert opposite effects while the effect of the transition states 'proton-in-the-middle' is considerable.
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Affiliation(s)
- Ibon Alkorta
- Instituto de Química Médica, CSIC, Juan de la Cierva, 3, E-28006 Madrid, Spain.
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19
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Golubev NS, Detering C, Smirnov SN, Shenderovich IG, Denisov GS, Limbach HH, Tolstoy PM. H/D isotope effects on NMR chemical shifts of nuclei involved in a hydrogen bridge of hydrogen isocyanide complexes with fluoride anion. Phys Chem Chem Phys 2009; 11:5154-9. [DOI: 10.1039/b900152b] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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20
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Joyce SA, Yates JR, Pickard CJ, Brown SP. Density Functional Theory Calculations of Hydrogen-Bond-Mediated NMR J Coupling in the Solid State. J Am Chem Soc 2008; 130:12663-70. [DOI: 10.1021/ja800419m] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Siân A. Joyce
- Tyndall National Institute, Lee Maltings, Prospect Row, Cork, Ireland, TCM Group, Cavendish Laboratory, University of Cambridge, 19 J. J. Thomson Avenue, Cambridge CB3 OHE, U.K., School of Physics and Astronomy, University of St. Andrews, North Haugh, St. Andrews KY16 9SS, U.K., and Department of Physics, University of Warwick, Coventry CV4 7AL, U.K
| | - Jonathan R. Yates
- Tyndall National Institute, Lee Maltings, Prospect Row, Cork, Ireland, TCM Group, Cavendish Laboratory, University of Cambridge, 19 J. J. Thomson Avenue, Cambridge CB3 OHE, U.K., School of Physics and Astronomy, University of St. Andrews, North Haugh, St. Andrews KY16 9SS, U.K., and Department of Physics, University of Warwick, Coventry CV4 7AL, U.K
| | - Chris J. Pickard
- Tyndall National Institute, Lee Maltings, Prospect Row, Cork, Ireland, TCM Group, Cavendish Laboratory, University of Cambridge, 19 J. J. Thomson Avenue, Cambridge CB3 OHE, U.K., School of Physics and Astronomy, University of St. Andrews, North Haugh, St. Andrews KY16 9SS, U.K., and Department of Physics, University of Warwick, Coventry CV4 7AL, U.K
| | - Steven P. Brown
- Tyndall National Institute, Lee Maltings, Prospect Row, Cork, Ireland, TCM Group, Cavendish Laboratory, University of Cambridge, 19 J. J. Thomson Avenue, Cambridge CB3 OHE, U.K., School of Physics and Astronomy, University of St. Andrews, North Haugh, St. Andrews KY16 9SS, U.K., and Department of Physics, University of Warwick, Coventry CV4 7AL, U.K
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21
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Alkorta I, Elguero J. Cation dinitrogen complexes [N(2)...X...N(2)]+, X+=H+, Li+, Na+, Be(2+), Mg(2+). SOLID STATE NUCLEAR MAGNETIC RESONANCE 2008; 34:105-109. [PMID: 18406109 DOI: 10.1016/j.ssnmr.2008.03.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2007] [Accepted: 03/04/2008] [Indexed: 05/26/2023]
Abstract
The complexes of dinitrogen with five cations (H(+), Li(+), Na(+), Be(2+) and Mg(2+)) up to four N(2) molecules have been calculated at the MP2/6-311++G(d,p) level. Energetic and geometric aspects have been determined together with absolute shieldings (GIAO). The atoms in molecules methodology has been used to analyze energy, charge and volume of these complexes.
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Affiliation(s)
- Ibon Alkorta
- Instituto de Química Médica (CSIC), Juan de la Cierva, 3, E-28006 Madrid, Spain.
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22
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Del Bene JE, Alkorta I, Elguero J. Ab Initio EOM-CCSD Spin−Spin Coupling Constants for Hydrogen-Bonded Formamide Complexes: Bridging Complexes with NH3, (NH3)2, H2O, (H2O)2, FH, and (FH)2. J Phys Chem A 2008; 112:6338-43. [DOI: 10.1021/jp801519v] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Janet E. Del Bene
- Department of Chemistry, Youngstown State University, Youngstown, Ohio 44555, and Instituto de Química Médica, CSIC, Juan de la Cierva 3, E-28006 Madrid, Spain
| | - Ibon Alkorta
- Department of Chemistry, Youngstown State University, Youngstown, Ohio 44555, and Instituto de Química Médica, CSIC, Juan de la Cierva 3, E-28006 Madrid, Spain
| | - José Elguero
- Department of Chemistry, Youngstown State University, Youngstown, Ohio 44555, and Instituto de Química Médica, CSIC, Juan de la Cierva 3, E-28006 Madrid, Spain
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23
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Afonin AV, Vashchenko AV, Ushakov IA, Zorina NV, Schmidt EY. Comparative analysis of hydrogen bonding with participation of the nitrogen, oxygen and sulfur atoms in the 2(2'-heteroaryl)pyrroles and their trifluoroacetyl derivatives based on the 1H, 13C, 15N spectroscopy and DFT calculations. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2008; 46:441-447. [PMID: 18318452 DOI: 10.1002/mrc.2197] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The N-H...X (X = N,O,S) intramolecular hydrogen bond in the series of 2(2'-heteroaryl)pyrroles and their trifluoroacetyl derivatives is examined by the (1)H, (13)C, (15)N spectroscopy and density functional theory (DFT) calculations. The influence of the hydrogen bond on coupling and shielding constants is considered. It is shown that the N-H...N intramolecular hydrogen bond causes a larger increase in the absolute size of the (1)J(N,H) coupling constant and a larger deshielding of the bridge proton than the N-H...O hydrogen bond. The effect of the N-H...S interaction on the (1)J(N,H) coupling constant and the shielding of the bridge proton is small. The NMR parameter changes in the series of the 2(2'-heteroaryl)pyrroles due to N-H...X hydrogen bond and the series of the 1-vinyl-2-(2'-heteroaryl)-pyrroles due to C-H...X hydrogen bond have the same order. The proximity of the nitrogen, oxygen or sulfur lone pair to the F...H hydrogen bridge quenches the trans-hydrogen bond spin-spin couplings (1h)J(F,H-1) and (2h)J(F,N).
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Affiliation(s)
- Andrei V Afonin
- Institute of Chemistry, Favorsky St 1, 664033 Irkutsk, Russia.
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24
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Del Bene JE, Alkorta I, Elguero J. Spin-spin coupling across intramolecular N-H(+)-N hydrogen bonds in models for proton sponges: an ab initio investigation. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2008; 46:457-463. [PMID: 18297741 DOI: 10.1002/mrc.2199] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Ab initio calculations have been performed to obtain structures and coupling constants (1)J(N-H), (1h)J(H-N), and (2h)J(N-N) for models of proton sponges with symmetric and asymmetric N-H(+)-N intramolecular hydrogen bonds (IMHBs). For a given model, the asymmetric structure has a lower energy, a longer N-N distance, and a hydrogen bond which has a greater deviation from linearity. The computed values of (2h)J(N-N) for the models are significantly less than predicted values based on the distance dependence of (2h)J(N-N) for complexes with intermolecular N-H(+)-N hydrogen bonds. However, the reduced values of (2h)J(N-N) cannot be attributed solely to the distortion of the hydrogen bond in the models, but also reflect differences in s electron populations at the nitrogens in both the ground state and the excited states which couple to it through the Fermi-contact (FC) operator. Values of (2h)J(N-N) for IMHBs can be related quadratically to the N-N distances in the models, and demonstrate that there is no discrepancy between computed values of (2h)J(N-N) at the short N-N distances found in these systems and experimental data for proton sponges.
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Affiliation(s)
- Janet E Del Bene
- Department of Chemistry, Youngstown State University, Youngstown, Ohio 44555, USA.
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25
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Pietrzak M, Try AC, Andrioletti B, Sessler JL, Anzenbacher P, Limbach HH. The largest 15N-15N coupling constant across an NHN hydrogen bond. Angew Chem Int Ed Engl 2008; 47:1123-6. [PMID: 18161718 DOI: 10.1002/anie.200704411] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Mariusz Pietrzak
- Institut für Chemie und Biochemie, Freie Universität Berlin, Takustr. 3, 14195 Berlin, Germany
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26
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Pietrzak M, Try A, Andrioletti B, Sessler J, Anzenbacher P, Limbach HH. The Largest15N–15N Coupling Constant Across an NHN Hydrogen Bond. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200704411] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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27
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Pietrzak M, Benedict C, Gehring H, Daltrozzo E, Limbach HH. NMR studies and DFT calculations of the symmetric intramolecular NHN-hydrogen bond of bis-(2-pyridyl)-acetonitrile: Isotope labeling strategy for the indirect 13C-detection of 15N15N couplings. J Mol Struct 2007. [DOI: 10.1016/j.molstruc.2007.04.023] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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28
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Vokacova Z, Sponer J, Sponer JE, Sychrovský V. Theoretical study of the scalar coupling constants across the noncovalent contacts in RNA base pairs: the cis- and trans-watson-crick/sugar edge base pair family. J Phys Chem B 2007; 111:10813-24. [PMID: 17713941 DOI: 10.1021/jp072822p] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The structure and function of RNA molecules are substantially affected by non-Watson-Crick base pairs actively utilizing the 2'-hydroxyl group of ribose. Here we correlate scalar coupling constants across the noncovalent contacts calculated for the cis- and trans-WC/SE (Watson-Crick/sugar edge) RNA base pairs with the geometry of base to base and sugar to base hydrogen bond(s). 23 RNA base pairs from the 32 investigated were found in RNA crystal structures, and the calculated scalar couplings are therefore experimentally relevant with regard to the binding patterns occurring in this class of RNA base pairs. The intermolecular scalar couplings 1hJ(N,H), 2hJ(N,N), 2hJ(C,H), and 3hJ(C,N) were calculated for the N-H...N and N-H...O=C base to base contacts and various noncovalent links between the sugar hydroxyl and RNA base. Also, the intramolecular 1J(N,H) and 2J(C,H) couplings were calculated for the amino or imino group of RNA base and the ribose 2'-hydroxyl group involved in the noncovalent interactions. The calculated scalar couplings have implications for validation of local geometry, show specificity for the amino and imino groups of RNA base involved in the linkage, and can be used for discrimination between the cis- and trans-WC/SE base pairs. The RNA base pairs within an isosteric subclass of the WC/SE binding patterns can be further sorted according to the scalar couplings calculated across different local noncovalent contacts. The effect of explicit water inserted in the RNA base pairs on the magnitude of the scalar couplings was calculated, and the data for discrimination between the water-inserted and direct RNA base pairs are presented. The calculated NMR data are significant for structural interpretation of the scalar couplings in the noncanonical RNA base pairs.
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Affiliation(s)
- Zuzana Vokacova
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo Square 2, 166 10 Prague 6, Czech Republic
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29
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Abstract
Density functional theory calculations were used to examine the effect of H-bond cooperativity on the magnitude of the NMR chemical shifts and spin-spin coupling constants in a C4h-symmetric G-quartet and in structures consisting of six cyanamide monomers. These included two ring structures (a planar C6h-symmetric structure and a nonplanar S6-symmetric structure) and two linear chain structures (a fully optimized planar Cs-symmetric chain and a planar chain structure where all intra- and intermolecular parameters were constrained to be identical). The NMR parameters were computed for the G-quartet and cyanamide structures, as well as for shorter fragments derived from these assemblies without reoptimization. In the ring structures and the chain with identical monomers, the intra- and intermolecular geometries of the cyanamides were identical, thereby allowing the study of cooperative effects in the absence of geometry changes. The magnitude of the |1JNH| coupling, 1H and 15N chemical shifts of the H-bonding amino N-H group, and the |h2JNN| H-bond coupling increased, whereas the size of the |1JNH| coupling of the non-H-bonded amino N-H bonds of the first amino group in the chain, which are roughly perpendicular to the H-bonding network, decreased in magnitude when H-bonding monomers were progressively added to extending ring or chain structures. These effects are attributed to electron redistribution induced by the presence of the nearby H-bonding guanine or cyanamide molecules.
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Affiliation(s)
- Tanja van Mourik
- Chemistry Department, University College London, 20 Gordon Street, London WC1H 0AJ, U.K.
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30
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Del Bene JE. Complexes with N-H(+)-P hydrogen bonds: structures, binding energies, and spin-spin coupling constants. J Phys Chem A 2007; 111:5509-14. [PMID: 17539616 DOI: 10.1021/jp0711491] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ab-initio MP2/aug'-cc-pVTZ calculations have been performed to determine the structures and binding energies of proton-bound complexes stabilized by N-H+-P hydrogen bonds and to investigate the nature of the proton-transfer coordinate in these systems. Double minima are found only when the difference between the protonation energies of the N and P bases is less than about 4 kcal/mol. The isomer in which the protonated nitrogen base is the donor lies lower on the potential surface and also has a greater binding energy relative to the corresponding isolated monomers. Equation-of-motion coupled cluster singles and doubles (EOM-CCSD) calculations have been employed to obtain one- and two-bond spin-spin coupling constants across these hydrogen bonds. Two-bond coupling constants (2h)J(N-P) correlate with N-P distances, irrespective of whether the donor ion is N-H+ or P-H+. One-bond coupling constants (1)J(N-H) and (1h)J(H-P) for complexes stabilized by N-H+...P hydrogen bonds correlate with corresponding distances, but similar correlations are not found for (1)J(P-H) and (1h)J(H-N) for complexes with P-H+...N hydrogen bonds. Negative values of (1h)K(H-N) and (1h)K(H-P) indicate that the hydrogen bonds in these complexes are traditional. Comparisons are made with complexes stabilized by N-H+-N and P-H+-P hydrogen bonds.
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Affiliation(s)
- Janet E Del Bene
- Department of Chemistry, Youngstown State University, Youngstown, OH 44555, USA.
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31
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Del Bene JE, Elguero J, Alkorta I. Probing P−H+−P Hydrogen Bonds: Structures, Binding Energies, and Spin−Spin Coupling Constants. J Phys Chem A 2007; 111:3416-22. [PMID: 17425291 DOI: 10.1021/jp068695z] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Ab initio MP2/aug'-cc-pVTZ calculations have been performed to determine the structures and binding energies of 22 open and 3 cyclic complexes formed from the sp2 [H(2)C=PH and HP=PH (cis and trans)] and sp3 [PH2(CH3) and PH3] hybridized phosphorus bases and their corresponding protonated ions. EOM-CCSD calculations have been carried out to obtain (31)P-(31)P and (31)P-(1)H coupling constants across P-H+-P hydrogen bonds. Two equilibrium structures with essentially linear hydrogen bonds have been found along the proton-transfer coordinate, except for complexes with P(CH3)H3+ as the proton donor to the sp2 bases. Although the isomer having the conjugate acid of the stronger base as the proton donor lies lower on the potential energy surface, it has a smaller binding energy relative to the corresponding isolated monomers than the isomer with the conjugate acid of the weaker base as the donor. The hydrogen bond of the latter has increased proton-shared character. All of the complexes are stabilized by traditional hydrogen bonds, as indicated by positive values of the reduced coupling constants (2h)K(P-P) and (1)K(P-H), and negative values of (1h)K(H-P). (2h)J(P-P) correlates with the P-P distance, a correlation determined primarily by the nature of the proton donor. For open complexes, (1)J(P-H) always increases relative to the isolated monomer, while (1h)J(H-P) is relatively small and negative. (2h)J(P-P) values are quite large in open complexes, but are much smaller in cyclic complexes in which the P-H+-P hydrogen bonds are nonlinear. Thus, experimental measurements of (2h)J(P-P) should be able to differentiate between open and cyclic complexes.
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Affiliation(s)
- Janet E Del Bene
- Department of Chemistry, Youngstown State University, Youngstown, Ohio 44555, USA.
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32
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van Mourik T, Dingley AJ. Geometry Dependence of Spin–Spin Couplings in Cyanamide by DFT Analysis. Chemphyschem 2007; 8:288-96. [PMID: 17221902 DOI: 10.1002/cphc.200600489] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
There have been numerous theoretical and experimental investigations examining NMR parameters related to non-amino N-H...N H-bonded moieties in both biological and chemical contexts. In contrast, little information on the geometry dependence of NMR parameters related to the biologically important H-bond donor amino group is available. Herein, the geometric dependencies of the one-bond amino N-H spin-spin coupling constants [(1)J(NH)] in the cyanamide monomer and dimer have been computed with B3LYP and the aug-cc-pVTZ-su0 basis set. In an isolated planar cyanamide molecule, the |(1)J(NH)| couplings were found to increase as the N-H bond lengthened. In contrast, in the planar cyanamide dimer the size of the H-bonded amino N-H coupling (|(1)J(N(d)H(d))|) decreased with increasing N(d)H(d) bond length. The |(1)J(N(d)H(d))| coupling was larger than the |(1)J(N(d)H(free))| coupling for N(d)H(d) distances up to 1.18 A (for a fixed N(d)H(free) distance of 1.006 A). Hence, the decrease of |(1)J(NH)| with increasing N-H distance, as well as the larger value of |(1)J(N(d)H(d))| compared to |(1)J(N(d)H(free))|, were only observed for situations where the amino group is involved in an H-bonding interaction. This is attributed to electron redistribution induced by the presence of the second cyanamide molecule. Similar electron-redistribution effects are thought to be responsible for the observed distance dependence of computed (1)J(NH) couplings of H-bonded amino groups in near-planar G-quartet structures. Here, the |(1)J(NH)| couplings of the amino N-H bonds decreased with increasing N-H bond length whereas the |(1)J(N(d)H(d))| couplings are approximately 7 Hz larger than the |(1)J(N(d)H(free))| couplings, despite the longer N(d)-H(d) bond length.
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Affiliation(s)
- Tanja van Mourik
- Chemistry Department, University College London, 20 Gordon Street, London WC1H 0AJ, UK.
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