Using Chemical Shift Perturbation to Characterise Ligand Binding ⇑ Mike P
Total Page:16
File Type:pdf, Size:1020Kb

Load more
Recommended publications
-
Ring Currents Modulate Optoelectronic Properties of Aromatic Chromophores at 25 T
Ring currents modulate optoelectronic properties of aromatic chromophores at 25 T Bryan Kudischa, Margherita Maiuria,b, Luca Morettia,b, Maria B. Oviedoa,c,d,e, Leon Wangf, Daniel G. Oblinskya, Robert K. Prud’hommef, Bryan M. Wongc, Stephen A. McGillg, and Gregory D. Scholesa,1 aDepartment of Chemistry, Princeton University, Princeton, NJ 08540; bDipartimento di Fisica, Politecnico di Milano, 20133 Milano, Italy; cDepartment of Chemical & Environmental Engineering, University of California, Riverside, CA 92521; dDepartment of Materials Science & Engineering, University of California, Riverside, CA 92521; eInstituto de Investigaciones Fisicoquímicas de Cordoba, Consejo Nacional de Investigaciones Científicas y Técnicas, Departamento de Química Teorica y Computacional, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, X5000HUA Córdoba, Argentina; fDepartment of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08540; and gNational High Magnetic Field Laboratory, Tallahassee, FL 32310 Edited by Catherine J. Murphy, University of Illinois at Urbana–Champaign, Urbana, IL, and approved April 1, 2020 (received for review October 16, 2019) The properties of organic molecules can be influenced by magnetic This perspective in many ways is inspired by some of the sa- fields, and these magnetic field effects are diverse. They range lient features that govern the magneto-optical responses in from inducing nuclear Zeeman splitting for structural determina- magnetic circular dichroism (MCD) spectroscopy. While best tion in NMR spectroscopy to polaron Zeeman splitting organic known for its ability to interrogate the degeneracy of electronic spintronics and organic magnetoresistance. A pervasive magnetic states, many electronic transitions will display a weak MCD due field effect on an aromatic molecule is the aromatic ring current, to the magnetic field-induced mixing of electronic states that which can be thought of as an induction of a circular current of gives rise to the B-terms, even in diamagnetic systems (19). -
4 Nuclear Magnetic Resonance
Chapter 4, page 1 4 Nuclear Magnetic Resonance Pieter Zeeman observed in 1896 the splitting of optical spectral lines in the field of an electromagnet. Since then, the splitting of energy levels proportional to an external magnetic field has been called the "Zeeman effect". The "Zeeman resonance effect" causes magnetic resonances which are classified under radio frequency spectroscopy (rf spectroscopy). In these resonances, the transitions between two branches of a single energy level split in an external magnetic field are measured in the megahertz and gigahertz range. In 1944, Jevgeni Konstantinovitch Savoiski discovered electron paramagnetic resonance. Shortly thereafter in 1945, nuclear magnetic resonance was demonstrated almost simultaneously in Boston by Edward Mills Purcell and in Stanford by Felix Bloch. Nuclear magnetic resonance was sometimes called nuclear induction or paramagnetic nuclear resonance. It is generally abbreviated to NMR. So as not to scare prospective patients in medicine, reference to the "nuclear" character of NMR is dropped and the magnetic resonance based imaging systems (scanner) found in hospitals are simply referred to as "magnetic resonance imaging" (MRI). 4.1 The Nuclear Resonance Effect Many atomic nuclei have spin, characterized by the nuclear spin quantum number I. The absolute value of the spin angular momentum is L =+h II(1). (4.01) The component in the direction of an applied field is Lz = Iz h ≡ m h. (4.02) The external field is usually defined along the z-direction. The magnetic quantum number is symbolized by Iz or m and can have 2I +1 values: Iz ≡ m = −I, −I+1, ..., I−1, I. -
Effect of Electronegative Elements on the NMR Chemical Shift in Some Simple R-X Organic Compounds
IOSR Journal of Applied Physics (IOSR-JAP) e-ISSN: 2278-4861.Volume 6, Issue 4 Ver. III (Jul-Aug. 2014), PP 45-56 www.iosrjournals.org Effect of electronegative elements on the NMR chemical shift in some simple R-X organic compounds Muhammad A. AL-Jalali1, Yahia M. Mahzia2 1Physics Department, Faculty of Science, Taif University, Taif, AL-Haweiah, , P. O. Box 888, Zip code 21974, Kingdom of Saudi Arabia 2Physics Department, Faculty of Science, Damascus University, Damascus, Syrian Arab Republic. Abstract: Organic halides and other organic compounds that contain electronegative elements, have a strong chemical shift and a brilliant NMR spectrum will prevail. Relationship between 1H, 13C NMR chemical shift and Electronegativity in some simple R-X organic compounds (X=F, Cl, Br, I, O, H, ...R=CH3 or CH3-CH2-) give nonlinear equation, as well as a power series equation appears between nuclear magnetogyric ratio, magnetic shielding constant and chemical shift, which are not included in the theoretical expressions. More investigations required to remove the discrepancy between the theoretical and the experimental results. Keywords: Electronegativity, chemical shift, shielding constant, magnetogyric ratio. I. Introduction Nuclear magnetic resonance, or NMR is a physical phenomenon was observed in 1945[1,2], which occurs when the nuclei of certain atoms, firstly, subject to nuclear Zeeman effect[3,4,5]will Precession with the Larmor frequency [6, 7]. Secondly, exposed to an oscillating electromagnetic field (radio waves), then if the radio wave frequency exactly matches the precession frequency, the resonance phenomenon will happen and this is the so-called nuclear magnetic resonance. However, experimentally, it has been noticed [8, 9, 10] that a nucleus may have a different resonant frequency for a given applied magnetic field in different chemical compounds, this difference in resonant frequency is called the chemical shift or sometimes fine structure. -
The Chemical Shift Chem 117 the Chemical Shift Key Questions (1) What Controls Proton Chemical Shifts? Eugene E
E. Kwan Lecture 2: The Chemical Shift Chem 117 The Chemical Shift Key Questions (1) What controls proton chemical shifts? Eugene E. Kwan January 26, 2012. H H H H 0.86 ppm 5.28 2.88 Br Scope of Lecture 16.4 proton chemical problem shift trends diamagnetic vs. (2) What controls carbon chemical shifts? solving paramagnetic O O shielding O CH2 H C OH the chemical 3 H3C CH3 basic DEPT 49.2 49.2 40.5 69.2 and COSY shift H-bonding and solvent (3) What are COSY and DEPT? What useful information effects spin-orbit coupling, can they give about a structure? carbon chemical effect of unsaturation shift trends 123 Helpful References 10 0 1. Nuclear Magnetic Resonance Spectroscopy... Lambert, J.B.; 1 Mazzola, E.P. Prentice-Hall, 2004. (Chapter 3) 2 2. The ABCs of FT-NMR Roberts, J.D. University Science Books, 2000. (Chapter 10) 3 3. Spectrometric Identification of Organic Compounds (7th ed.) Silverstein, R.M.; Webster, F.X.; Kiemle, D.J. Wiley, 2005. (useful charts in the appendices of chapters 2-4) 10 4. Organic Structural Spectroscopy Lambert, J.B.; Shurvell, H.F.; Lightner, D.A.; Cooks, R.G. Prentice-Hall, 1998. I thank Professors William F. Reynolds (Toronto) and Gene Mazzola (Maryland/FDA) for providing some useful 5. Organic Structure Analysis Crews, P. Rodriguez, J.; Jaspars, material for this lecture. The section on chemical shifts M. Oxford University Press, 1998. is based on the discussion in Chapter 3 of reference 1. E. Kwan Lecture 2: The Chemical Shift Chem 117 Proton Chemical Shifts Clearly, the regions overlap: reference: Lambert and Mazzola, Chapter 3. -
NMR Chemical Shifts of Common Laboratory Solvents As Trace Impurities
7512 J. Org. Chem. 1997, 62, 7512-7515 NMR Chemical Shifts of Common Laboratory Solvents as Trace Impurities Hugo E. Gottlieb,* Vadim Kotlyar, and Abraham Nudelman* Department of Chemistry, Bar-Ilan University, Ramat-Gan 52900, Israel Received June 27, 1997 In the course of the routine use of NMR as an aid for organic chemistry, a day-to-day problem is the identifica- tion of signals deriving from common contaminants (water, solvents, stabilizers, oils) in less-than-analyti- cally-pure samples. This data may be available in the literature, but the time involved in searching for it may be considerable. Another issue is the concentration dependence of chemical shifts (especially 1H); results obtained two or three decades ago usually refer to much Figure 1. Chemical shift of HDO as a function of tempera- more concentrated samples, and run at lower magnetic ture. fields, than today’s practice. 1 13 We therefore decided to collect H and C chemical dependent (vide infra). Also, any potential hydrogen- shifts of what are, in our experience, the most popular bond acceptor will tend to shift the water signal down- “extra peaks” in a variety of commonly used NMR field; this is particularly true for nonpolar solvents. In solvents, in the hope that this will be of assistance to contrast, in e.g. DMSO the water is already strongly the practicing chemist. hydrogen-bonded to the solvent, and solutes have only a negligible effect on its chemical shift. This is also true Experimental Section for D2O; the chemical shift of the residual HDO is very NMR spectra were taken in a Bruker DPX-300 instrument temperature-dependent (vide infra) but, maybe counter- (300.1 and 75.5 MHz for 1H and 13C, respectively). -
Quantitative Analysis of Biomolecular NMR Spectra: a Prerequisite for the Determination of the Structure and Dynamics of Biomolecules
Current Organic Chemistry, 2006, 10, 00-00 1 Quantitative Analysis of Biomolecular NMR Spectra: A Prerequisite for the Determination of the Structure and Dynamics of Biomolecules Thérèse E. Malliavin* Laboratoire de Biochimie Théorique, CNRS UPR 9080, Institut de Biologie PhysicoChimique, 13 rue P. et M. Curie, 75 005 Paris, France. Abstract: Nuclear Magnetic Resonance (NMR) became during the two last decades an important method for biomolecular structure determination. NMR permits to study biomolecules in solution and gives access to the molecular flexibility at atomic level on a complete structure: in that respect, it is occupying a unique place in structural biology. During the first years of its development, NMR was trying to meet the requirements previously defined in X-ray crystallography. But, NMR then started to determine its own criteria for the definition of a structure. Indeed, the atomic coordinates of an NMR structure are calculated using restraints on geometrical parameters (angles and distances) of the structure, which are only indirectly related to atom positions: in that respect, NMR and X-ray crystallography are very different. The indirect relation between the NMR measurements and the molecular structure and dynamics makes critical the precision and the interpretation of the NMR parameters and the development of quantitative analysis methods. The methods published since 1997 for liquid-NMR of proteins are reviewed here. First, methods for structure determination are presented, as well as methods for spectral assignment and for structure quality assessment. Second, the quantitative analysis of structure mobility is reviewed. 1. INTRODUCTION parameters is fuzzy, because each NMR parameter is Nuclear Magnetic Resonance (NMR) became at the depending not only on the structure, but also on the internal beginning of 90's, a method of choice for structural biology dynamics of the molecule, and these two aspects are difficult in solution. -
HASH: a Program to Accurately Predict Protein H Shifts from Neighboring Backbone Shifts
J Biomol NMR DOI 10.1007/s10858-012-9693-7 ARTICLE a HASH: a program to accurately predict protein H shifts from neighboring backbone shifts Jianyang Zeng • Pei Zhou • Bruce Randall Donald Received: 25 October 2012 / Accepted: 5 December 2012 Ó Springer Science+Business Media Dordrecht 2012 Abstract Chemical shifts provide not only peak identities atoms (i.e., adjacent atoms in the sequence), can remedy for analyzing nuclear magnetic resonance (NMR) data, but the above dilemmas, and hence advance NMR-based also an important source of conformational information for structural studies of proteins. By specifically exploiting the studying protein structures. Current structural studies dependencies on chemical shifts of nearby backbone requiring Ha chemical shifts suffer from the following atoms, we propose a novel machine learning algorithm, a a limitations. (1) For large proteins, the H chemical shifts called HASH, to predict H chemical shifts. HASH combines can be difficult to assign using conventional NMR triple- a new fragment-based chemical shift search approach with resonance experiments, mainly due to the fast transverse a non-parametric regression model, called the generalized relaxation rate of Ca that restricts the signal sensitivity. (2) additive model, to effectively solve the prediction problem. Previous chemical shift prediction approaches either We demonstrate that the chemical shifts of nearby back- require homologous models with high sequence similarity bone atoms provide a reliable source of information for or rely heavily on accurate backbone and side-chain predicting accurate Ha chemical shifts. Our testing results structural coordinates. When neither sequence homologues on different possible combinations of input data indicate nor structural coordinates are available, we must resort to that HASH has a wide rage of potential NMR applications in other information to predict Ha chemical shifts. -
Automatic 13C Chemical Shift Reference Correction for Unassigned Protein NMR Spectra
Journal of Biomolecular NMR https://doi.org/10.1007/s10858-018-0202-5 ARTICLE Automatic 13C chemical shift reference correction for unassigned protein NMR spectra Xi Chen1,2 · Andrey Smelter1,3,4 · Hunter N. B. Moseley1,2,3,4,5 Received: 10 April 2018 / Accepted: 1 August 2018 © The Author(s) 2018 Abstract Poor chemical shift referencing, especially for 13C in protein Nuclear Magnetic Resonance (NMR) experiments, fundamen- tally limits and even prevents effective study of biomacromolecules via NMR, including protein structure determination and analysis of protein dynamics. To solve this problem, we constructed a Bayesian probabilistic framework that circumvents the limitations of previous reference correction methods that required protein resonance assignment and/or three-dimensional protein structure. Our algorithm named Bayesian Model Optimized Reference Correction (BaMORC) can detect and correct 13C chemical shift referencing errors before the protein resonance assignment step of analysis and without three-dimensional structure. By combining the BaMORC methodology with a new intra-peaklist grouping algorithm, we created a combined method called Unassigned BaMORC that utilizes only unassigned experimental peak lists and the amino acid sequence. Unassigned BaMORC kept all experimental three-dimensional HN(CO)CACB-type peak lists tested within ± 0.4 ppm of the correct 13C reference value. On a much larger unassigned chemical shift test set, the base method kept 13C chemical shift ref- erencing errors to within ± 0.45 ppm at a 90% confidence interval. With chemical shift assignments, Assigned BaMORC can detect and correct 13C chemical shift referencing errors to within ± 0.22 at a 90% confidence interval. Therefore, Unassigned BaMORC can correct 13C chemical shift referencing errors when it will have the most impact, right before protein resonance assignment and other downstream analyses are started. -
Article Is Available Online Is One of the Most Comprehensive Ways to Envision Such at Doi:10.5194/Bg-13-2257-2016-Supplement
Biogeosciences, 13, 2257–2277, 2016 www.biogeosciences.net/13/2257/2016/ doi:10.5194/bg-13-2257-2016 © Author(s) 2016. CC Attribution 3.0 License. Molecular characterization of dissolved organic matter from subtropical wetlands: a comparative study through the analysis of optical properties, NMR and FTICR/MS Norbert Hertkorn1, Mourad Harir1, Kaelin M. Cawley2, Philippe Schmitt-Kopplin1, and Rudolf Jaffé2 1Helmholtz Zentrum München, German Research Center for Environmental Health, Research Unit Analytical Biogeochemistry (BGC), Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany 2Southeast Environmental Research Center, and Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL 33199, USA Correspondence to: Rudolf Jaffé (jaffer@fiu.edu) Received: 23 July 2015 – Published in Biogeosciences Discuss.: 25 August 2015 Revised: 22 December 2015 – Accepted: 7 February 2016 – Published: 19 April 2016 Abstract. Wetlands provide quintessential ecosystem ser- relative disparity was largest between the Everglades long- vices such as maintenance of water quality, water supply and short-hydroperiod samples, whereas Pantanal and Oka- and biodiversity, among others; however, wetlands are also vango samples were more alike among themselves. Other- among the most threatened ecosystems worldwide. Natural wise, molecular divergence was most obvious in the case dissolved organic matter (DOM) is an abundant and criti- of unsaturated protons (δH > 5 ppm). 2-D NMR spectroscopy cal component in wetland biogeochemistry. This study de- for a particular sample revealed a large richness of aliphatic scribes the first detailed, comparative, molecular characteri- and unsaturated substructures, likely derived from microbial zation of DOM in subtropical, pulsed, wetlands, namely the sources such as periphyton in the Everglades. -
Cycloosmathioborane Compounds: Other Manifestations of the Hückel
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Repositorio Universidad de Zaragoza Communication Cite This: Inorg. Chem. XXXX, XXX, XXX−XXX pubs.acs.org/IC Cycloosmathioborane Compounds: Other Manifestations of the Hückel Aromaticity † ‡ † † Miguel A. Esteruelas,*, Israel Fernandez,́ Cristina García-Yebra, Jaime Martín, † and Enrique Oñate † Departamento de Química Inorganica,́ Instituto de Síntesis Química y Catalisiś Homogenea,́ Centro de Innovacioń en Química Avanzada (ORFEO−CINQA), Universidad de Zaragoza, CSIC, 50009 Zaragoza, Spain ‡ Departamento de Química Organicá I, Facultad de Ciencias Químicas, ORFEO−CINQA, Universidad Complutense de Madrid, 28040 Madrid, Spain *S Supporting Information have reported EP2 triangles (E = Ge, Sn, Pb), which are ABSTRACT: The discovery of cycloosmathioborane stabilized within the coordination sphere of a sterically protected compounds is reported. These species, which are prepared diniobium unit,13 whereas Guha’s group has computationally by the simultaneous dehydrogenation of a trihydride predicted that the substitution of a B atom in the triangle fi 2− ff hydrogensul de osmium(IV) complex and a BH3NHR2 [B3H3] by a group 15 element should a ord neutral aromatic − − − 14 amine borane, bear an Os S B three-membered ring, H2B2XH rings (X = N, P). Herein, we take one step forward in being a manifestation of the 4n +2Hückel aromaticity in this fascinating field by reporting the preparation and full which n = 0 and where the two π electrons of the ring are characterization of the first aromatic triangles having three provided by the S atom. different vertexes, namely, two main-group elements, S and B, and a transition metal with its associated ligands. -
FULL PAPER Hückel's Rule of Aromaticity Categorizes
FULL PAPER Hückel’s Rule of Aromaticity Categorizes Aromatic closo Boron Hydride Clusters Jordi Poater,[a,b] Miquel Solà,*[c] Clara Viñas,[d] and Francesc Teixidor*[d] Abstract: A direct connection is established between tridimensional P, N, or other incorporating transition or lanthanide metal aromatic closo boron hydride clusters and planar aromatic fragments. Consequently, the icosahedron or bicapped square antiprism are very relevant geometrical features in BHs and, by [n]annulenes for medium and large size boron clusters. In particular, extension, to other areas in which clusters are significant, e.g. our results prove the existence of a link between the two-dimensional Zintl phases. Hückel rule followed by aromatic [n]-annulenes and Wade-Mingos’ 2- In the last few years, we have given evidence that the concept rule of three-dimensional aromaticity applied to the aromatic [BnHn] of aromaticity, in terms of planar or tridimensional aromaticity, was closo boron hydride clusters. Our results show that closo boron not too distant, and that most probably -aromaticity and 3D hydride clusters can be categorized into different series according to aromaticity were based on the same grounds.[4] This is why we the n value of the Hückel (4n+2) rule. The distinct categories studied named them as the two sides of the same coin.[4b] To reach such in this work correspond to values of n = 1, 2, and 3. Each category conclusion we compared the conventional (4n+2) planar organic increases in geometrical difficulty but, more importantly, it is possible cyclic compounds with closo BHs. The aromaticity properties of to associate each category with the number of pentagonal layers in planar organic cyclic compounds had been demonstrated by their stability, hydrogenation experimental studies, substitution but not the structure perpendicular to the main axis. -
Measuring T1 and T2 Relaxation Times
Relaxation Measurements Two Relaxation Mechanisms 90° pulse T1: Spin‐lattice or longitudinal relaxation is the average lifetime of the nuclei in the higher spin state T2: Spin‐spin or transverse relaxation corresponds to a de‐coherence of the transverse nuclear spin magnetization Spin‐Lattice Relaxation Time or T1 • Any factor which slows molecular motion (e.g. increasing solution viscosity, aggregation, or rigidifying the molecule) shortens the spin‐lattice relaxation time • A short T1 favors sensitivity but too short can result in line broadening and degradation of resolution since T2 cannot be longer than T1 • 3 principal magnetic interactions that contribute to T1 relaxation of spin ½ nuclei: o Dipole‐dipole interaction ‐ the nucleus experiences a fluctuating field due to the motions of neighboring dipoles, unpaired electrons, or other nuclei o Chemical shift anisotropy ‐ chemical shielding of the nucleus is a function of molecular orientation with respect to B0 field direction o Spin rotation interaction –small magnetic fields are induced at the nucleus as a molecule reorients; this field fluctuates because the motions are not uniform but proceed by a series of small jumps • Small amounts of paramagnetic substances speed up relaxation • Inversion recovery experiment measures T1 T1 Measurement: Inversion Recovery Parameters to note & Optimize • To change the value of the delay, d7, a variable delay list must be created. • In the acquisition parameters a VDLIST can be generated which contains values that typically cover a time range which extends past vdlist the expected T1 value. 0.05 0.5 Iz = I0(1‐2exp(‐d7/T1) 1.0 1.5 ln(I0‐Iz) = ln(2I0)‐d7/T1 2 Tnull = T1*ln2 4 6 8 Spin‐Spin Relaxation Time or T2 • T1 = T2 when molecular tumbling is fast compared with the Larmor frequency; this is the condition for small molecules.