Literature DB >> 20806897

Decomposition of vibrational shifts of nitriles into electrostatic and hydrogen-bonding effects.

Aaron T Fafarman1, Paul A Sigala, Daniel Herschlag, Steven G Boxer.   

Abstract

Infrared (IR) band shifts of isolated vibrational transitions can serve as quantitative and directional probes of local electrostatic fields, due to the vibrational Stark effect. However, departures from the Stark model can arise when the probe participates in specific, chemical interactions, such as direct hydrogen bonding. We present a method to identify and correct for these departures based on comparison of (13)C n class="Chemical">NMR chemical shifts and IR frequencies each calibrated in turn by a solvatochromic model. We demonstrate how the tandem use of these experimental observables can be applied to a thiocyanate-modified protein, ketosteroid isomerase, and show, by comparison to structural models, that changes in electrostatic field can be measured within the complex protein environment even in the background of direct hydrogen bonding to the probe.

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Year:  2010        PMID: 20806897      PMCID: PMC2943212          DOI: 10.1021/ja104573b

Source DB:  PubMed          Journal:  J Am Chem Soc        ISSN: 0002-7863            Impact factor:   15.419


  20 in total

1.  Do ligand binding and solvent exclusion alter the electrostatic character within the oxyanion hole of an enzymatic active site?

Authors:  Paul A Sigala; Aaron T Fafarman; Patrick E Bogard; Steven G Boxer; Daniel Herschlag
Journal:  J Am Chem Soc       Date:  2007-09-14       Impact factor: 15.419

2.  Computational Modeling of the Nitrile Stretching Vibration of 5-Cyanoindole in Water.

Authors:  Matthias M Waegele; Feng Gai
Journal:  J Phys Chem Lett       Date:  2010-02-01       Impact factor: 6.475

3.  Binding of 2-naphthols to D38E mutants of 3-oxo-Delta 5-steroid isomerase: variation of ligand ionization state with the nature of the electrophilic component.

Authors:  I P Petrounia; G Blotny; R M Pollack
Journal:  Biochemistry       Date:  2000-01-11       Impact factor: 3.162

4.  A test of the role of electrostatic interactions in determining the CO stretch frequency in carbonmonoxymyoglobin.

Authors:  S M Decatur; S G Boxer
Journal:  Biochem Biophys Res Commun       Date:  1995-07-06       Impact factor: 3.575

5.  Cyanylated Cysteine: A Covalently Attached Vibrational Probe of Protein-Lipid Contacts.

Authors:  Heather A McMahon; Katherine N Alfieri; Katherine A A Clark; Casey H Londergan
Journal:  J Phys Chem Lett       Date:  2010-02-12       Impact factor: 6.475

6.  Using nitrile-derivatized amino acids as infrared probes of local environment.

Authors:  Zelleka Getahun; Cheng-Yen Huang; Ting Wang; Brenda De León; William F DeGrado; Feng Gai
Journal:  J Am Chem Soc       Date:  2003-01-15       Impact factor: 15.419

7.  Nitrile groups as vibrational probes: calculations of the CN infrared absorption line shape of acetonitrile in water and tetrahydrofuran.

Authors:  Beth A Lindquist; Steven A Corcelli
Journal:  J Phys Chem B       Date:  2008-04-26       Impact factor: 2.991

8.  Nitrile and thiocyanate IR probes: quantum chemistry calculation studies and multivariate least-square fitting analysis.

Authors:  Jun-Ho Choi; Kwang-Im Oh; Hochan Lee; Chewook Lee; Minhaeng Cho
Journal:  J Chem Phys       Date:  2008-04-07       Impact factor: 3.488

9.  Hydrogen bond coupling in the ketosteroid isomerase active site.

Authors:  Paul A Sigala; Jose M M Caaveiro; Dagmar Ringe; Gregory A Petsko; Daniel Herschlag
Journal:  Biochemistry       Date:  2009-07-28       Impact factor: 3.162

10.  The catalytic power of ketosteroid isomerase investigated by computer simulation.

Authors:  Isabella Feierberg; Johan Aqvist
Journal:  Biochemistry       Date:  2002-12-31       Impact factor: 3.162

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  44 in total

Review 1.  Vibrational Spectroscopic Map, Vibrational Spectroscopy, and Intermolecular Interaction.

Authors:  Carlos R Baiz; Bartosz Błasiak; Jens Bredenbeck; Minhaeng Cho; Jun-Ho Choi; Steven A Corcelli; Arend G Dijkstra; Chi-Jui Feng; Sean Garrett-Roe; Nien-Hui Ge; Magnus W D Hanson-Heine; Jonathan D Hirst; Thomas L C Jansen; Kijeong Kwac; Kevin J Kubarych; Casey H Londergan; Hiroaki Maekawa; Mike Reppert; Shinji Saito; Santanu Roy; James L Skinner; Gerhard Stock; John E Straub; Megan C Thielges; Keisuke Tominaga; Andrei Tokmakoff; Hajime Torii; Lu Wang; Lauren J Webb; Martin T Zanni
Journal:  Chem Rev       Date:  2020-06-29       Impact factor: 60.622

2.  Quantitative, directional measurement of electric field heterogeneity in the active site of ketosteroid isomerase.

Authors:  Aaron T Fafarman; Paul A Sigala; Jason P Schwans; Timothy D Fenn; Daniel Herschlag; Steven G Boxer
Journal:  Proc Natl Acad Sci U S A       Date:  2012-01-17       Impact factor: 11.205

3.  Selective incorporation of nitrile-based infrared probes into proteins via cysteine alkylation.

Authors:  Hyunil Jo; Robert M Culik; Ivan V Korendovych; William F Degrado; Feng Gai
Journal:  Biochemistry       Date:  2010-11-17       Impact factor: 3.162

4.  Site-Specific Spectroscopic Reporters of the Local Electric Field, Hydration, Structure, and Dynamics of Biomolecules.

Authors:  Matthias M Waegele; Robert M Culik; Feng Gai
Journal:  J Phys Chem Lett       Date:  2011-09-23       Impact factor: 6.475

5.  Solvatochromism and the solvation structure of benzophenone.

Authors:  Justin E Elenewski; John C Hackett
Journal:  J Chem Phys       Date:  2013-06-14       Impact factor: 3.488

6.  Heterogeneous and Highly Dynamic Interface in Plastocyanin-Cytochrome f Complex Revealed by Site-Specific 2D-IR Spectroscopy.

Authors:  Sashary Ramos; Amanda L Le Sueur; Rachel E Horness; Jonathan T Specker; Jessica A Collins; Katherine E Thibodeau; Megan C Thielges
Journal:  J Phys Chem B       Date:  2019-02-21       Impact factor: 2.991

7.  Detection of electron tunneling across plasmonic nanoparticle-film junctions using nitrile vibrations.

Authors:  Hao Wang; Kun Yao; John A Parkhill; Zachary D Schultz
Journal:  Phys Chem Chem Phys       Date:  2017-02-22       Impact factor: 3.676

8.  Solvent-induced infrared frequency shifts in aromatic nitriles are quantitatively described by the vibrational Stark effect.

Authors:  Nicholas M Levinson; Stephen D Fried; Steven G Boxer
Journal:  J Phys Chem B       Date:  2012-04-05       Impact factor: 2.991

9.  Measuring electrostatic fields in both hydrogen-bonding and non-hydrogen-bonding environments using carbonyl vibrational probes.

Authors:  Stephen D Fried; Sayan Bagchi; Steven G Boxer
Journal:  J Am Chem Soc       Date:  2013-07-18       Impact factor: 15.419

10.  Site-selective Characterization of Src Homology 3 Domain Molecular Recognition with Cyanophenylalanine Infrared Probes.

Authors:  Rachel E Horness; Edward J Basom; Megan C Thielges
Journal:  Anal Methods       Date:  2015-04-08       Impact factor: 2.896

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