1
|
Stare J, Gradišek A, Seliger J. Nuclear quadrupole resonance supported by periodic quantum calculations: a sensitive tool for precise structural characterization of short hydrogen bonds. Phys Chem Chem Phys 2020; 22:27681-27689. [PMID: 33237040 DOI: 10.1039/d0cp04710d] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Systems with short hydrogen bonds (H-bonds) are notoriously difficult to describe even using cutting edge experimental techniques supported by advanced computational protocols. One of the most challenging issues is the highly dislocated H-bonded proton, which is typically smeared over a large area, featuring complex dynamics governed by pronounced nuclear quantum effects. Thus, in combination with experimental results, these systems offer a rich platform for the benchmarking of various computational approaches and methods. Herein, we present a methodology combining experimental and computational assessment of H-bond observables probed by the nuclear quadrupole resonance technique. Focusing on the case of picolinic acid N-oxide featuring one of the shortest known hydrogen bonds (ROO ∼ 2.425 Å), we compare the predictions of nuclear quadrupole coupling constants (NQCCs) for a series of computational models differing in fine structural details of the H-bond. By comparing the computed 14N and 17O NQCCs with the measured ones and by analyzing the sensitivity of NQCCs to H-bond geometry variations, we demonstrate that NQCCs represent a very sensitive probe for H-bond geometry, particularly the proton location, thereby offering, in conjunction with computations, an accurate and reliable tool for the fine structural characterization of short H-bonds. Importantly, the present methodology is a good compromise between accuracy and computational cost.
Collapse
Affiliation(s)
- Jernej Stare
- Theory Department, National Institute of Chemistry, Ljubljana, Slovenia.
| | | | | |
Collapse
|
2
|
Seif Eddine M, Biaso F, Arias‐Cartin R, Pilet E, Rendon J, Lyubenova S, Seduk F, Guigliarelli B, Magalon A, Grimaldi S. Probing the Menasemiquinone Binding Mode to Nitrate Reductase A by Selective2H and15N Labeling, HYSCORE Spectroscopy, and DFT Modeling. Chemphyschem 2017; 18:2704-2714. [DOI: 10.1002/cphc.201700571] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 07/04/2017] [Indexed: 11/05/2022]
Affiliation(s)
| | | | | | - Eric Pilet
- Aix Marseille University, CNRS, BIP Marseille France
- Faculté de Biologie, University Pierre et Marie Curie Paris France
| | - Julia Rendon
- Aix Marseille University, CNRS, BIP Marseille France
| | | | - Farida Seduk
- Aix Marseille University, CNRS, LCB Marseille France
| | | | - Axel Magalon
- Aix Marseille University, CNRS, LCB Marseille France
| | | |
Collapse
|
3
|
Pietrzyńska M, Zembrzuska J, Tomczak R, Mikołajczyk J, Rusińska-Roszak D, Voelkel A, Buchwald T, Jampílek J, Lukáč M, Devínsky F. Experimental and in silico investigations of organic phosphates and phosphonates sorption on polymer-ceramic monolithic materials and hydroxyapatite. Eur J Pharm Sci 2016; 93:295-303. [DOI: 10.1016/j.ejps.2016.08.033] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Revised: 08/13/2016] [Accepted: 08/18/2016] [Indexed: 01/01/2023]
|
4
|
Abstract
The structure and dynamics of the bound water in barium chlorate monohydrate were studied with (17)O nuclear magnetic resonance (NMR) spectroscopy in samples that are stationary and spinning at the magic-angle in magnetic fields ranging from 14.1 to 21.1 T. (17)O NMR parameters of the water were determined, and the effects of torsional oscillations of the water molecule on the (17)O quadrupolar coupling constant (CQ) were delineated with variable temperature MAS NMR. With decreasing temperature and reduction of the librational motion, we observe an increase in the experimentally measured CQ explaining the discrepancy between experiments and predictions from density functional theory. In addition, at low temperatures and in the absence of (1)H decoupling, we observe a well-resolved (1)H-(17)O dipole splitting in the spectra, which provides information on the structure of the H2O molecule. The splitting arises because of the homogeneous nature of the coupling between the two (1)H-(17)O dipoles and the (1)H-(1)H dipole.
Collapse
Affiliation(s)
- Eric G. Keeler
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | | | - Robert G. Griffin
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| |
Collapse
|
5
|
Löwenstein J, Lauterbach L, Teutloff C, Lenz O, Bittl R. Active Site of the NAD(+)-Reducing Hydrogenase from Ralstonia eutropha Studied by EPR Spectroscopy. J Phys Chem B 2015. [PMID: 26214595 DOI: 10.1021/acs.jpcb.5b04144] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Pulsed ENDOR and HYSCORE measurements were carried out to characterize the active site of the oxygen-tolerant NAD(+)-reducing hydrogenase of Ralstonia eutropha. The catalytically active Nia-C state exhibits a bridging hydride between iron and nickel in the active site, which is photodissociated upon illumination. Its hyperfine coupling is comparable to that of standard hydrogenases. In addition, a histidine residue could be identified, which shows hyperfine and nuclear quadrupole parameters in significant variance from comparable histidine residues that are conserved in standard [NiFe] hydrogenases, and might be related to the O2 tolerance of the enzyme.
Collapse
Affiliation(s)
- Julia Löwenstein
- Fachbereich Physik, Freie Universität Berlin , Arnimallee 14, 14195 Berlin, Germany
| | - Lars Lauterbach
- Institut für Chemie, Sekr. PC14, Technische Universität Berlin , Strasse des 17. Juni 135, 10623 Berlin, Germany
| | - Christian Teutloff
- Fachbereich Physik, Freie Universität Berlin , Arnimallee 14, 14195 Berlin, Germany
| | - Oliver Lenz
- Institut für Chemie, Sekr. PC14, Technische Universität Berlin , Strasse des 17. Juni 135, 10623 Berlin, Germany
| | - Robert Bittl
- Fachbereich Physik, Freie Universität Berlin , Arnimallee 14, 14195 Berlin, Germany
| |
Collapse
|
6
|
Taguchi AT, O'Malley PJ, Wraight CA, Dikanov SA. Hyperfine and nuclear quadrupole tensors of nitrogen donors in the Q(A) site of bacterial reaction centers: correlation of the histidine N(δ) tensors with hydrogen bond strength. J Phys Chem B 2014; 118:9225-37. [PMID: 25026433 PMCID: PMC4126732 DOI: 10.1021/jp5051029] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
X-
and Q-band pulsed EPR spectroscopy was applied to study the
interaction of the QA site semiquinone (SQA)
with nitrogens from the local protein environment in natural abundance 14N and in 15N uniformly labeled photosynthetic
reaction centers of Rhodobacter sphaeroides. The hyperfine and nuclear quadrupole tensors for His-M219 Nδ and Ala-M260 peptide nitrogen (Np) were
estimated through simultaneous simulation of the Q-band 15N Davies ENDOR, X- and Q-band 14,15N HYSCORE, and X-band 14N three-pulse ESEEM spectra, with support from DFT calculations.
The hyperfine coupling constants were found to be a(14N) = 2.3 MHz, T = 0.3 MHz for His-M219
Nδ and a(14N) = 2.6 MHz, T = 0.3 MHz for Ala-M260 Np. Despite that His-M219
Nδ is established as the stronger of the two H-bond
donors, Ala-M260 Np is found to have the larger value of a(14N). The nuclear quadrupole coupling constants
were estimated as e2Qq/4h = 0.38 MHz, η = 0.97 and e2Qq/4h = 0.74 MHz, η = 0.59 for His-M219 Nδ and Ala-M260 Np, respectively. An analysis of the available
data on nuclear quadrupole tensors for imidazole nitrogens found in
semiquinone-binding proteins and copper complexes reveals these systems
share similar electron occupancies of the protonated nitrogen orbitals.
By applying the Townes–Dailey model, developed previously for
copper complexes, to the semiquinones, we find the asymmetry parameter
η to be a sensitive probe of the histidine Nδ–semiquinone hydrogen bond strength. This is supported by
a strong correlation observed between η and the isotropic coupling
constant a(14N) and is consistent with
previous computational works and our own semiquinone-histidine model
calculations. The empirical relationship presented here for a(14N) and η will provide an important
structural characterization tool in future studies of semiquinone-binding
proteins.
Collapse
Affiliation(s)
- Alexander T Taguchi
- Center for Biophysics and Computational Biology, §Department of Biochemistry, and ∥Department of Veterinary Clinical Medicine, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | | | | | | |
Collapse
|
7
|
Frielingsdorf S, Fritsch J, Schmidt A, Hammer M, Löwenstein J, Siebert E, Pelmenschikov V, Jaenicke T, Kalms J, Rippers Y, Lendzian F, Zebger I, Teutloff C, Kaupp M, Bittl R, Hildebrandt P, Friedrich B, Lenz O, Scheerer P. Reversible [4Fe-3S] cluster morphing in an O2-tolerant [NiFe] hydrogenase. Nat Chem Biol 2014; 10:378-85. [DOI: 10.1038/nchembio.1500] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Accepted: 03/13/2014] [Indexed: 12/27/2022]
|
8
|
Taguchi AT, O'Malley PJ, Wraight CA, Dikanov SA. Nuclear hyperfine and quadrupole tensor characterization of the nitrogen hydrogen bond donors to the semiquinone of the QB site in bacterial reaction centers: a combined X- and S-band (14,15)N ESEEM and DFT study. J Phys Chem B 2014; 118:1501-9. [PMID: 24437652 PMCID: PMC3983398 DOI: 10.1021/jp411023k] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
The
secondary quinone anion radical QB– (SQB) in reaction centers of Rhodobacter
sphaeroides interacts with Nδ of
His-L190 and Np (peptide nitrogen) of Gly-L225 involved
in hydrogen bonds to the QB carbonyls. In this work, S-band
(∼3.6 GHz) ESEEM was used with the aim of obtaining a complete
characterization of the nuclear quadrupole interaction (nqi) tensors
for both nitrogens by approaching the cancelation condition between
the isotropic hyperfine coupling and 14N Zeeman frequency
at lower microwave frequencies than traditional X-band (9.5 GHz).
By performing measurements at S-band, we found a dominating contribution
of Nδ in the form of a zero-field nqi triplet at
0.55, 0.92, and 1.47 MHz, defining the quadrupole coupling constant K = e2qQ/4h = 0.4 MHz and associated asymmetry parameter η =
0.69. Estimates of the hyperfine interaction (hfi) tensors for Nδ and Np were obtained from simulations of
1D and 2D 14,15N X-band and three-pulse 14N
S-band spectra with all nuclear tensors defined in the SQB g-tensor coordinate system. From simulations, we conclude that the
contribution of Np to the S-band spectrum is suppressed
by its strong nqi and weak isotropic hfi comparable to the level of
hyperfine anisotropy, despite the near-cancelation condition for Np at S-band. The excellent agreement between our EPR simulations
and DFT calculations of the nitrogen hfi and nqi tensors to SQB is promising for the future application of powder ESEEM to
full tensor characterizations.
Collapse
Affiliation(s)
- Alexander T Taguchi
- Center for Biophysics and Computational Biology, ‡Department of Biochemistry, §Department of Veterinary Clinical Medicine, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | | | | | | |
Collapse
|
9
|
Elmi MM, Kaykhaei AA, Elmi F. Density functional theory study of nitrogen-14 nuclear quadrupole coupling parameters of L-histidine: hydrogen-bonded system. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2012; 50:314-319. [PMID: 22415677 DOI: 10.1002/mrc.3809] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2011] [Revised: 01/22/2012] [Accepted: 02/13/2012] [Indexed: 05/31/2023]
Abstract
The calculations of nitrogen-14 nuclear quadrupole parameters, nuclear quadrupole coupling constant, χ, and asymmetry parameter, η, of L-His were done in two distinct environments: one as a free fully optimized molecule, an isolated molecule with the geometrical parameters taken from X-ray, and the other in the orthorhombic and monoclinic solid states. The most probable interacting molecules with the central molecule in the crystalline phase were considered in the hexameric clusters to include hydrogen-bonding effects in the calculations. The computations were performed with PW91P86/6-31++G** and B3LYP6-31++G** methods using the Gaussian 98 program. The good agreement between the nitrogen-14 quadrupole parameters of the free His and imidazole molecules with their microwave available data demonstrates that the applied level of theory and the 6-31++G** basis set are suitable to obtain reliable electric field gradient values. In the solid state, the shifts of quadrupole coupling parameters from the monomer to the solid phase are reasonably well reproduced for the amino and imino sites of imidazole ring in a hexameric cluster. That implies the fact that the hexameric cluster worked effectively to generate the results which are compatible with the experiment. The quadrupole coupling constant values of -N(+) H(3) group are in fair agreement with the experiment. This discrepancy is due to the absences of vibrational effects and the rotation of -N(+) H(3) group around N-C(α) bond.
Collapse
Affiliation(s)
- Maryam Mitra Elmi
- Cellular and Molecular Biology Research Center, Babol University of Medical Sciences, PO Box: 4717647745, Babol, Iran
| | | | | |
Collapse
|
10
|
Grimaldi S, Arias-Cartin R, Lanciano P, Lyubenova S, Szenes R, Endeward B, Prisner TF, Guigliarelli B, Magalon A. Determination of the proton environment of high stability Menasemiquinone intermediate in Escherichia coli nitrate reductase A by pulsed EPR. J Biol Chem 2011; 287:4662-70. [PMID: 22190684 DOI: 10.1074/jbc.m111.325100] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Escherichia coli nitrate reductase A (NarGHI) is a membrane-bound enzyme that couples quinol oxidation at a periplasmically oriented Q-site (Q(D)) to proton release into the periplasm during anaerobic respiration. To elucidate the molecular mechanism underlying such a coupling, endogenous menasemiquinone-8 intermediates stabilized at the Q(D) site (MSQ(D)) of NarGHI have been studied by high-resolution pulsed EPR methods in combination with (1)H2O/2H2O exchange experiments. One of the two non-exchangeable proton hyperfine couplings resolved in hyperfine sublevel correlation (HYSCORE) spectra of the radical displays characteristics typical from quinone methyl protons. However, its unusually small isotropic value reflects a singularly low spin density on the quinone carbon α carrying the methyl group, which is ascribed to a strong asymmetry of the MSQ(D) binding mode and consistent with single-sided hydrogen bonding to the quinone oxygen O1. Furthermore, a single exchangeable proton hyperfine coupling is resolved, both by comparing the HYSCORE spectra of the radical in 1H2O and 2H2O samples and by selective detection of the exchanged deuterons using Q-band 2H Mims electron nuclear double resonance (ENDOR) spectroscopy. Spectral analysis reveals its peculiar characteristics, i.e. a large anisotropic hyperfine coupling together with an almost zero isotropic contribution. It is assigned to a proton involved in a short ∼1.6 Å in-plane hydrogen bond between the quinone O1 oxygen and the Nδ of the His-66 residue, an axial ligand of the distal heme b(D). Structural and mechanistic implications of these results for the electron-coupled proton translocation mechanism at the Q(D) site are discussed, in light of the unusually high thermodynamic stability of MSQ(D).
Collapse
Affiliation(s)
- Stéphane Grimaldi
- Unité de Bioénergétique et Ingénierie des Protéines (UPR9036), Institut de Microbiologie de la Méditerranée, CNRS and Aix-Marseille University, 13009 Marseille, France.
| | | | | | | | | | | | | | | | | |
Collapse
|
11
|
Ab initio DFT study of bisphosphonate derivatives as a drug for inhibition of cancer: NMR and NQR parameters. J Mol Model 2011; 18:929-36. [DOI: 10.1007/s00894-011-1114-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2010] [Accepted: 04/28/2011] [Indexed: 11/26/2022]
|
12
|
MacMillan F, Kacprzak S, Hellwig P, Grimaldi S, Michel H, Kaupp M. Elucidating mechanisms in haemcopperoxidases: The high-affinity QHbinding site in quinol oxidase as studied by DONUT-HYSCOREspectroscopy and density functional theory. Faraday Discuss 2011; 148:315-44; discussion 421-41. [DOI: 10.1039/c005149g] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
13
|
Grimaldi S, Arias-Cartin R, Lanciano P, Lyubenova S, Endeward B, Prisner TF, Magalon A, Guigliarelli B. Direct evidence for nitrogen ligation to the high stability semiquinone intermediate in Escherichia coli nitrate reductase A. J Biol Chem 2009; 285:179-87. [PMID: 19892705 DOI: 10.1074/jbc.m109.060251] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The membrane-bound heterotrimeric nitrate reductase A (NarGHI) catalyzes the oxidation of quinols in the cytoplasmic membrane of Escherichia coli and reduces nitrate to nitrite in the cytoplasm. The enzyme strongly stabilizes a menasemiquinone intermediate at a quinol oxidation site (Q(D)) located in the vicinity of the distal heme b(D). Here molecular details of the interaction between the semiquinone radical and the protein environment have been provided using advanced multifrequency pulsed EPR methods. (14)N and (15)N ESEEM and HYSCORE measurements carried out at X-band ( approximately 9.7 GHz) on the wild-type enzyme or the enzyme uniformly labeled with (15)N nuclei reveal an interaction between the semiquinone and a single nitrogen nucleus. The isotropic hyperfine coupling constant A(iso)((14)N) approximately 0.8 MHz shows that it occurs via an H-bond to one of the quinone carbonyl group. Using (14)N ESEEM and HYSCORE spectroscopies at a lower frequency (S-band, approximately 3.4 GHz), the (14)N nuclear quadrupolar parameters of the interacting nitrogen nucleus (kappa = 0.49, eta = 0.50) were determined and correspond to those of a histidine N(delta), assigned to the heme b(D) ligand His-66 residue. Moreover S-band (15)N ESEEM spectra enabled us to directly measure the anisotropic part of the nitrogen hyperfine interaction (T((15)N) = 0.16 MHz). A distance of approximately 2.2 Abetween the carbonyl oxygen and the nitrogen could then be calculated. Mechanistic implications of these results are discussed in the context of the peculiar properties of the menasemiquinone intermediate stabilized at the Q(D) site of NarGHI.
Collapse
Affiliation(s)
- Stéphane Grimaldi
- Unité de Bioénergétique et Ingénierie des Protéines (UPR9036), Institut de Microbiologie de laMéditerranée, CNRS and Aix-Marseille Université, 31 chemin Joseph Aiguier, 13402 Marseille Cedex 20, France.
| | | | | | | | | | | | | | | |
Collapse
|
14
|
Ames WM, Larsen SC. Density Functional Theory Investigation of EPR Parameters for Tetragonal Cu(II) Model Complexes with Oxygen Ligands. J Phys Chem A 2009; 113:4305-12. [DOI: 10.1021/jp810924j] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- William M. Ames
- Department of Chemistry, The University of Iowa, Iowa City, Iowa 52242
| | - Sarah C. Larsen
- Department of Chemistry, The University of Iowa, Iowa City, Iowa 52242
| |
Collapse
|
15
|
Insight into the copper coordination environment in the prion protein through density functional theory calculations of EPR parameters. J Biol Inorg Chem 2009; 14:547-57. [DOI: 10.1007/s00775-009-0469-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2008] [Accepted: 01/16/2009] [Indexed: 10/21/2022]
|
16
|
Ames WM, Larsen SC. DFT calculations of the EPR parameters for Cu(ii) DETA imidazole complexes. Phys Chem Chem Phys 2009; 11:8266-74. [DOI: 10.1039/b905750a] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
17
|
Javadian S, Araghi R. A DFT study of the 67Zn, 14N and 2H electric field gradient tensors in Zinc(II)–4-MeIm complexes and extrapolation to superoxide dismutase. J Mol Graph Model 2009; 27:620-7. [DOI: 10.1016/j.jmgm.2008.10.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2008] [Revised: 10/08/2008] [Accepted: 10/09/2008] [Indexed: 10/21/2022]
|
18
|
Dikanov SA, Holland JT, Endeward B, Kolling DRJ, Samoilova RI, Prisner TF, Antony R. C. Hydrogen bonds between nitrogen donors and the semiquinone in the Qi-site of the bc1 complex. J Biol Chem 2007; 282:25831-41. [PMID: 17616531 PMCID: PMC3060708 DOI: 10.1074/jbc.m702333200] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The ubisemiquinone stabilized at the Qi-site of the bc1 complex of Rhodobacter sphaeroides forms a hydrogen bond with a nitrogen from the local protein environment, tentatively identified as ring N from His-217. The interactions of 14N and 15N have been studied by X-band (approximately 9.7 GHz) and S-band (3.4 GHz) pulsed EPR spectroscopy. The application of S-band spectroscopy has allowed us to determine the complete nuclear quadrupole tensor of the 14N involved in H-bond formation and to assign it unambiguously to the Nepsilon of His-217. This tensor has distinct characteristics in comparison with H-bonds between semiquinones and Ndelta in other quinone-processing sites. The experiments with 15N showed that the Nepsilon of His-217 was the only nitrogen carrying any considerable unpaired spin density in the ubiquinone environment, and allowed calculation of the isotropic and anisotropic couplings with the Nepsilon of His-217. From these data, we could estimate the unpaired spin density transferred onto 2s and 2p orbitals of nitrogen and the distance from the nitrogen to the carbonyl oxygen of 2.38+/-0.13A. The hyperfine coupling of other protein nitrogens with semiquinone is <0.1 MHz. This did not exclude the nitrogen of the Asn-221 as a possible hydrogen bond donor to the methoxy oxygen of the semiquinone. A mechanistic role for this residue is supported by kinetic experiments with mutant strains N221T, N221H, N221I, N221S, N221P, and N221D, all of which showed some inhibition but retained partial turnover.
Collapse
Affiliation(s)
- Sergei A. Dikanov
- Department of Veterinary Clinical Medicine, University of Illinois, Urbana, Illinois 61801
| | - J. Todd Holland
- Center for Biophysics and Computational Biology, University of Illinois, Urbana, Illinois 61801
| | - Burkhard Endeward
- J. W. Goethe Universitaät, Institut für Physikalische und Theoretische Chemie, Max-von-Laue-Strasse 7, D-60438 Frankfurt, Germany
| | - Derrick R. J. Kolling
- Center for Biophysics and Computational Biology, University of Illinois, Urbana, Illinois 61801
| | - Rimma I. Samoilova
- Institute of Chemical Kinetics and Combustion, Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Thomas F. Prisner
- J. W. Goethe Universitaät, Institut für Physikalische und Theoretische Chemie, Max-von-Laue-Strasse 7, D-60438 Frankfurt, Germany
| | - Crofts Antony R.
- Center for Biophysics and Computational Biology, University of Illinois, Urbana, Illinois 61801
- Department of Biochemistry, University of Illinois, Urbana, Illinois 61801
| |
Collapse
|
19
|
Fritscher J, Hrobárik P, Kaupp M. Computational studies of EPR parameters for paramagnetic molybdenum complexes. II. Larger MoV systems relevant to molybdenum enzymes. Inorg Chem 2007; 46:8146-61. [PMID: 17725345 DOI: 10.1021/ic070341e] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The careful validation of modern density functional methods for the computation of electron paramagnetic resonance (EPR) parameters in molybdenum complexes has been extended to a number of low-symmetry MoV systems that model molybdoenzyme active sites. Both g and hyperfine tensors tend to be reproduced best by hybrid density functionals with about 30-40% exact-exchange admixture, with no particular spin contamination problems encountered. Spin-orbit corrections to hyperfine tensors are mandatory for quantitative and, in some cases, even for qualitative agreement. The g11 (g||) component of the g tensor tends to come out too positive when spin-orbit coupling is included only to leading order in perturbation theory. Compared to single-crystal experiments, the calculations reproduce both g- and hyperfine-tensor orientations well, both relative to each other and to the molecular framework. This is significant, as simulations of the EPR spectra of natural-abundance frozen-solution samples frequently do not allow a reliable determination of the hyperfine tensors. These may now be extracted based on the quantum-chemically calculated parameters. In a number of cases, revised simulations of the experimental spectra have brought theory and experiment into substantially improved agreement. Systems with two terminal oxo ligands, and to some extent with an oxo and a sulfido ligand, have been confirmed to exhibit particularly large negative Deltag33 shifts and thus large g anisotropies. This is discussed in the context of the experimental data for xanthine oxidase.
Collapse
Affiliation(s)
- Jörg Fritscher
- Institute of Physical and Theoretical Chemistry and Center for Biological Magnetic Resonance, J. W. Goethe University of Frankfurt, Max-von-Laue-Str. 7, D-60438 Frankfurt, Germany.
| | | | | |
Collapse
|
20
|
Fritscher J, Hrobarik P, Kaupp M. Computational Studies of Electron Paramagnetic Resonance Parameters for Paramagnetic Molybdenum Complexes. 1. Method Validation on Small and Medium-Sized Systems. J Phys Chem B 2007; 111:4616-29. [PMID: 17408258 DOI: 10.1021/jp070638y] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A variety of density functional methods have been evaluated in the computation of electronic g-tensors and molybdenum hyperfine couplings for systems ranging from the Mo atom through MoIIIN, [MoVOCl4]-, and [MoVOF5]2- to two larger MoV complexes MoXLCl2 (X=O, S; L=tris(3,5-dimethylpyrazolyl)hydroborate anion). In particular, the influence of the molybdenum basis set and of various exchange-correlation functionals with variable admixtures of Hartree-Fock exchange on the computed EPR parameters have been evaluated in detail. Careful basis-set studies have provided a moderate-sized 12s6p5d all-electron basis on molybdenum that gives hyperfine tensors in excellent agreement with much larger basis sets and that will be useful for calculations on larger systems. The best agreement with experimental data for both hyperfine and g-tensors is obtained with hybrid functionals containing approximately 30-40% Hartree-Fock exchange. Only for MoSLCl2 does increasing spin contamination with increasing exact-exchange admixture restrict the achievable computational accuracy. In all cases, spin-orbit corrections to the hyperfine tensors are sizable and have to be included in accurate calculations. Scalar relativistic effects enhance the isotropic Mo hyperfine coupling by approximately 15-20%. Two-component g-tensor calculations with variational inclusion of spin-orbit coupling show that the Deltag parallel components in [MoVOCl4]- and [MoVOF5]2- depend on higher-order spin-orbit contributions and are thus described insufficiently by the usual second-order perturbation approaches. Computed orientations of g- and hyperfine tensors relative to each other and to the molecular framework for the MoXLCl2 complexes provide good agreement between theory and single-crystal electron paramagnetic resonance experiments. In these cases, the hyperfine tensor orientations are influenced only slightly by spin-orbit effects.
Collapse
Affiliation(s)
- Jörg Fritscher
- Institute of Physical and Theoretical Chemistry, J. W. Goethe University of Frankfurt, and Center for Biological Magnetic Resonance, Max-von-Laue-Strasse 7, D-60438 Frankfurt, Germany.
| | | | | |
Collapse
|
21
|
Choi MY, Miller RE. Infrared Laser Spectroscopy of Imidazole Complexes in Helium Nanodroplets: Monomer, Dimer, and Binary Water Complexes. J Phys Chem A 2006; 110:9344-51. [PMID: 16869682 DOI: 10.1021/jp0624146] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Infrared laser spectroscopy has been used to characterize imidazole (IM), imidazole dimer (IMD), and imidazole-water (IMW) binary systems formed in helium nanodroplets. The experimental results are compared with ab initio calculations reported here. Vibrational transition moment angles provide conclusive assignments for the various complexes studied here, including IM, one isomer of IMD, and two isomers of the IMW binary complexes.
Collapse
Affiliation(s)
- Myong Yong Choi
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA.
| | | |
Collapse
|
22
|
|
23
|
Sinnecker S, Rajendran A, Klamt A, Diedenhofen M, Neese F. Calculation of Solvent Shifts on Electronic g-Tensors with the Conductor-Like Screening Model (COSMO) and Its Self-Consistent Generalization to Real Solvents (Direct COSMO-RS). J Phys Chem A 2006; 110:2235-45. [PMID: 16466261 DOI: 10.1021/jp056016z] [Citation(s) in RCA: 477] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The conductor-like screening model (COSMO) was used to investigate the solvent influence on electronic g-values of organic radicals. The previously studied diphenyl nitric oxide and di-tert-butyl nitric oxide radicals were taken as test cases. The calculations employed spin-unrestricted density functional theory and the BP and B3LYP density functionals. The g-tensors were calculated as mixed second derivative properties with respect to the external magnetic field and the electron magnetic moment. The first-order response of the Kohn-Sham orbitals with respect to the external magnetic field was determined through the coupled-perturbed DFT approach. The spin-orbit coupling operator was treated using an accurate multicenter spin-orbit mean-field (SOMF) approach. Provided that important hydrogen bonds are explicitly modeled by a supermolecule approach and that the basis set is sufficiently saturated, the COSMO calculations lead to accurate predictions of isotropic g-shifts with deviations of not more than 100 ppm relative to experiment. Very accurate results were obtained by employing a recently developed self-consistent modification of the COSMO method to real solvents (COSMO-RS), which we briefly introduce in this paper as direct COSMO-RS (D-COSMO-RS). This model gives isotropic g-shifts of similar high accuracy for water without using the supermolecule approach. This is an important result because it solves many of the problems associated with the supermolecule approach such as local minima and the choice of a suitable model system. Thus, the self-consistent D-COSMO-RS incorporates some specific solvation effects into continuum models, in particular it appears to successfully model the effects of hydrogen bonding. Although not yet widely validated, this opens a novel approach for the calculation of properties which so far only could be calculated by the inclusion of explicit solvent molecules in continuum solvation methods.
Collapse
Affiliation(s)
- Sebastian Sinnecker
- Max-Planck-Institut für Bioanorganische Chemie, Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany
| | | | | | | | | |
Collapse
|
24
|
Sinnecker S, Flores M, Lubitz W. Protein–cofactor interactions in bacterial reaction centers from Rhodobacter sphaeroides R-26: Effect of hydrogen bonding on the electronic and geometric structure of the primary quinone. A density functional theory study. Phys Chem Chem Phys 2006; 8:5659-70. [PMID: 17149487 DOI: 10.1039/b612568a] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The effect of hydrogen bonding to the primary quinone (Q(A) and Q(*)(-)(A)) in bacterial reaction centers was studied using density functional theory (DFT) calculations. The charge neutral state Q(A) was investigated by optimizing the hydrogen atom positions of model systems extracted from 15 different X-ray structures. From this analysis, mean values of the H-bond lengths and directions were derived. It was found that the N(delta)-H of His M219 forms a shorter H-bond to Q(A) than the N-H of Ala M260. The H-bond of His M219 is linear and more twisted out of the quinone plane. The radical anion Q(*)(-)(A) in the protein environment was investigated by using a mixed quantum mechanics/molecular mechanics (QM/MM) approach. Two geometry optimizations with a different number of flexible atoms were performed. H-bond lengths were obtained and spectroscopic parameters calculated, i.e. the hyperfine and nuclear quadrupole couplings of magnetic nuclei coupled to the radical. Good agreement was found with the results provided by EPR/ENDOR spectroscopy. This implies that the calculated lengths and directions of the H-bonds to Q(*)(-)(A) are reliable values. From a comparison of the neutral and reduced state of Q(A) it was concluded that the H-bond distances are shortened by approximately 0.17 Angstroms (His M219) and approximately 0.13 Angstroms (Ala M260) upon single reduction of the quinone. It is shown that the point-dipole approximation can not be used for an estimation of H-bond lengths from measured hyperfine couplings in a system with out-of-plane H-bonding. In contrast, the evaluation of the nuclear quadrupole couplings of (2)H nuclei substituted in the hydrogen bonds yields H-bond lengths close to the values that were deduced from DFT geometry optimizations. The significance of hydrogen bonding to the quinone cofactors in biological systems is discussed.
Collapse
Affiliation(s)
- Sebastian Sinnecker
- Max-Planck-Institut für Bioanorganische Chemie, Stiftstrasse 34-36, D-45470, Mülheim an der Ruhr, Germany
| | | | | |
Collapse
|