Transition Metal Activation and Functionalization of Carbon-Hydrogen Bonds
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Covalent and Noncovalent Intermediates of an NAD Utilizing Enzyme, Human CD38
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector Chemistry & Biology Article Covalent and Noncovalent Intermediates of an NAD Utilizing Enzyme, Human CD38 Qun Liu,1 Irina A. Kriksunov,1 Hong Jiang,2 Richard Graeff,4 Hening Lin,2 Hon Cheung Lee,4,5,* and Quan Hao1,3,5,* 1MacCHESS, Cornell High Energy Synchrotron Source 2Department of Chemistry and Chemical Biology 3School of Applied & Engineering Physics Cornell University, Ithaca, NY 14853, USA 4Department of Pharmacology, University of Minnesota, Minneapolis, MN 55455, USA 5Department of Physiology, University of Hong Kong, Hong Kong, China *Correspondence: [email protected] (H.C.L.), [email protected] (Q.H.) DOI 10.1016/j.chembiol.2008.08.007 SUMMARY These processes are known to have important cellular and physiological functions in DNA repair (Lombard et al., 2005; Enzymatic utilization of nicotinamide adenine dinu- Michan and Sinclair, 2007), transcriptional regulation (Blander cleotide (NAD) has increasingly been shown to have and Guarente, 2004), cellular differentiation and proliferation, fundamental roles in gene regulation, signal trans- aging (Hassa et al., 2006), and calcium signaling (Lee, 2001; duction, and protein modification. Many of the pro- Lee et al., 1999). cesses require the cleavage of the nicotinamide moi- Although NAD is a substrate for multiple enzymes, the initial ety from the substrate and the formation of a reactive steps of the cleavage and release of the nicotinamide moiety are conserved. The nature of the subsequent intermediates intermediate. Using X-ray crystallography, we show formed, on the other hand, has been a widely debatable issue. -
Recommending Hartree-Fock Theory with London- Dispersion and Basis
Recommending Hartree-Fock Theory with London- Dispersion and Basis-Set-Superposition Corrections for the Optimization or Quantum Refinement of Protein Structures Lars Goerigk,a* Charles A. Collyer,b Jeffrey R. Reimersc,d* a School of Chemistry, The University of Melbourne, Parkville, Victoria 3010, Australia b School of Molecular Bioscience, The University of Sydney, Sydney, New South Wales 2006, Australia c School of Physics and Advanced Materials, The University of Technology, Sydney, NSW 2007, Australia d Centre for Quantum and Molecular Structure, College of Sciences, Shanghai University, Shanghai 200444, China 1 ABSTRACT We demonstrate the importance of properly accounting for London-dispersion and basis-set superposition-error (BSSE) in quantum-chemical optimizations of protein structures, factors that are often still neglected in contemporary applications. We optimize a portion of an ensemble of conformationally flexible lysozyme structures obtained from highly accurate X-ray crystallography data that serves as a reliable benchmark. We not only analyze root-mean-square deviations from the experimental Cartesian coordinates, but, for the first time, also demonstrate how London-dispersion and BSSE influence crystallographic R factors. Our conclusions parallel recent recommendations for the optimization of small gas-phase peptide structures made by some of the present authors: Hartree-Fock theory extended with Grimme’s recent dispersion and BSSE corrections (HF-D3-gCP) is superior to popular density-functional-theory (DFT) approaches. Not only are statistical errors on average lower with HF-D3-gCP, but also its convergence behavior is much better. In particular, we show that the BP86/6-31G* approach should not be relied upon as a black-box method, despite its widespread use, as its success is based on an unpredictable cancellation of errors. -
2.#Water;#Acid.Base#Reac1ons
8/24/15 BIOCH 755: Biochemistry I Fall 2015 2.#Water;#Acid.base#reac1ons# Jianhan#Chen# Office#Hour:#M#1:30.2:30PM,#Chalmers#034# Email:#[email protected]# Office:#785.2518# 2.1#Physical#Proper1es#of#Water# • Key$Concepts$2.1$ – Water#molecules,#which#are#polar,#can#form#hydrogen#bonds#with# other#molecules.# – In#ice,#water#molecules#are#hydrogen#bonded#in#a#crystalline#array,#but# in#liquid#water,#hydrogen#bonds#rapidly#break#and#re.form#in#irregular# networks.# – The#aTrac1ve#forces#ac1ng#on#biological#molecules#include#ionic# interac1ons,#hydrogen#bonds,#and#van#der#Waals#interac1ons.# – Polar#and#ionic#substances#can#dissolve#in#water.# (c)#Jianhan#Chen# 2# 1 8/24/15 2.1#Physical#Proper1es#of#Water# • Key$Concepts$2.1$ – The#hydrophobic#effect#explains#the#exclusion#of#nonpolar#groups#as#a# way#to#maximize#the#entropy#of#water#molecules.# – Amphiphilic#substances#form#micelles#or#bilayers#that#hide#their# hydrophobic#groups#while#exposing#their#hydrophilic#groups#to#water.# – Molecules#diffuse#across#membranes#which#are#permeable#to#them# from#regions#of#higher#concentra1on#to#regions#of#lower# concentra1on.# – In#dialysis,#solutes#diffuse#across#a#semipermeable#membrane#from# regions#of#higher#concentra1on#to#regions#of#lower#concentra1on.# (c)#Jianhan#Chen# 3# Human#Body#Mass#Composi1on# (c)#Jianhan#Chen# 4 2 8/24/15 Structure#of#Water# (c)#Jianhan#Chen# 5 Water#Hydrogen#Bonding# ~1.8 Å, 180o Acceptor Donor (c)#Jianhan#Chen# 6# 3 8/24/15 Typical#Bond#Energies# (c)#Jianhan#Chen# 7# Hydrogen#bond#networks#of#water/ice# (c)#Jianhan#Chen# -
Mechanism of the Cooperative Si–H Bond Activation at Ru–S Bonds† Cite This: Chem
Chemical Science View Article Online EDGE ARTICLE View Journal | View Issue Mechanism of the cooperative Si–H bond activation at Ru–S bonds† Cite this: Chem. Sci.,2015,6,4324 a a ab b Timo Stahl, Peter Hrobarik,´ * C. David F. Konigs,¨ Yasuhiro Ohki, Kazuyuki Tatsumi,b Sebastian Kemper,a Martin Kaupp,a Hendrik F. T. Klare*a and Martin Oestreich*a The nature of the hydrosilane activation mediated by ruthenium(II) thiolate complexes of type [(R3P)- + F À Ru(SDmp)] [BAr 4] is elucidated by an in-depth experimental and theoretical study. The combination of various ruthenium(II) thiolate complexes and tertiary hydrosilanes under variation of the phosphine ligand and the substitution pattern at the silicon atom is investigated, providing detailed insight into the activation mode. The mechanism of action involves reversible heterolytic splitting of the Si–H bond across the polar Ru–S bond without changing the oxidation state of the metal, generating a ruthenium(II) hydride and sulfur-stabilized silicon cations, i.e. metallasilylsulfonium ions. These stable yet highly reactive adducts, which serve as potent silicon electrophiles in various catalytic transformations, are fully Creative Commons Attribution 3.0 Unported Licence. characterized by systematic multinuclear NMR spectroscopy. The structural assignment is further verified by successful isolation and crystallographic characterization of these key intermediates. Quantum- chemical analyses of diverse bonding scenarios are in excellent agreement with the experimental findings. Moreover, the calculations reveal that formation of the hydrosilane adducts proceeds via barrierless electrophilic activation of the hydrosilane by sterically controlled h1 (end-on) or h2 (side-on) coordination of the Si–H bond to the Lewis acidic metal center, followed by heterolytic cleavage of the Received 21st March 2015 Si–H bond through a concerted four-membered transition state. -
FOCUS REVIEW Transition Metal Mediated Cleavage of C-C Bonds
FOCUS REVIEW Transition Metal Mediated Cleavage of C-C Bonds in Aromatic Rings Martin Jakoobi,[a] and Alexey G. Sergeev*[a] [a] Title(s), Initial(s), Surname(s) of Author(s) including Corresponding Author(s) Department Institution Address 1 E-mail: [b] Title(s), Initial(s), Surname(s) of Author(s) Department Institution Address 2 Supporting information for this article is given via a link at the end of For internalthe document. use,((Please please delete dothis textnot if notdelete. appropriate)) Submitted_Manuscript FOCUS REVIEW Abstract: Metal-mediated cleavage of aromatic C-C bonds has a 1.2. Challenges in metal mediated cleavage of aromatic C-C range of potential synthetic applications: from direct coal liquefaction bonds to synthesis of natural products. However, in contrast to the activation of aromatic C-H bonds, which has already been widely In contrast to activation of aromatic C-H bonds, which is now studied and exploited in diverse set of functionalization reactions, widely used in organic synthesis, activation of aromatic C-C cleavage of aromatic C-C bonds is still Terra Incognita. This focus bonds is still a challenging and largely unexplored area.[1, 8] review summarizes the recent progress in this field and outlines key Activation of strong aromatic C-C bonds requires harsh reaction challenges to be overcome to develop synthetic methods based on conditions, and occurs with poor chemoselectivity (C-H bonds this fundamental organometallic transformation. are activated preferentially) and regioselectivity (different kinds of aromatic C-C bonds can be activated indiscriminately), which limits synthetic applications of this promising transformation. The 1. -
A New Way for Probing Bond Strength J
A New Way for Probing Bond Strength J. Klein, H. Khartabil, J.C. Boisson, J. Contreras-Garcia, Jean-Philip Piquemal, E. Henon To cite this version: J. Klein, H. Khartabil, J.C. Boisson, J. Contreras-Garcia, Jean-Philip Piquemal, et al.. A New Way for Probing Bond Strength. Journal of Physical Chemistry A, American Chemical Society, 2020, 124 (9), pp.1850-1860. 10.1021/acs.jpca.9b09845. hal-02377737 HAL Id: hal-02377737 https://hal.archives-ouvertes.fr/hal-02377737 Submitted on 27 Mar 2021 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. A New Way for Probing Bond Strength Johanna Klein,y Hassan Khartabil,y Jean-Charles Boisson,z Julia Contreras-Garc´ıa,{ Jean-Philip Piquemal,{ and Eric H´enon∗,y yInstitut de Chimie Mol´eculaire de Reims UMR CNRS 7312, Universit´ede Reims Champagne-Ardenne, Moulin de la Housse 51687 Reims Cedex 02 BP39 (France) zCReSTIC EA 3804, Universit´ede Reims Champagne-Ardenne, Moulin de la Housse 51687 Reims Cedex 02 BP39 (France) {Sorbonne Universit´es,UPMC, Laboratoire de Chimie Th´eoriqueand UMR CNRS 7616, 4 Pl Jussieu, 75252 Paris Cedex 05(France) E-mail: [email protected] Phone: +33(3)26918497 1 Abstract The covalent chemical bond is intimately linked to electron sharing between atoms. -
Bond Distances and Bond Orders in Binuclear Metal Complexes of the First Row Transition Metals Titanium Through Zinc
Metal-Metal (MM) Bond Distances and Bond Orders in Binuclear Metal Complexes of the First Row Transition Metals Titanium Through Zinc Richard H. Duncan Lyngdoh*,a, Henry F. Schaefer III*,b and R. Bruce King*,b a Department of Chemistry, North-Eastern Hill University, Shillong 793022, India B Centre for Computational Quantum Chemistry, University of Georgia, Athens GA 30602 ABSTRACT: This survey of metal-metal (MM) bond distances in binuclear complexes of the first row 3d-block elements reviews experimental and computational research on a wide range of such systems. The metals surveyed are titanium, vanadium, chromium, manganese, iron, cobalt, nickel, copper, and zinc, representing the only comprehensive presentation of such results to date. Factors impacting MM bond lengths that are discussed here include (a) n+ the formal MM bond order, (b) size of the metal ion present in the bimetallic core (M2) , (c) the metal oxidation state, (d) effects of ligand basicity, coordination mode and number, and (e) steric effects of bulky ligands. Correlations between experimental and computational findings are examined wherever possible, often yielding good agreement for MM bond lengths. The formal bond order provides a key basis for assessing experimental and computationally derived MM bond lengths. The effects of change in the metal upon MM bond length ranges in binuclear complexes suggest trends for single, double, triple, and quadruple MM bonds which are related to the available information on metal atomic radii. It emerges that while specific factors for a limited range of complexes are found to have their expected impact in many cases, the assessment of the net effect of these factors is challenging. -
Electron Ionization
Chapter 6 Chapter 6 Electron Ionization I. Introduction ......................................................................................................317 II. Ionization Process............................................................................................317 III. Strategy for Data Interpretation......................................................................321 1. Assumptions 2. The Ionization Process IV. Types of Fragmentation Pathways.................................................................328 1. Sigma-Bond Cleavage 2. Homolytic or Radical-Site-Driven Cleavage 3. Heterolytic or Charge-Site-Driven Cleavage 4. Rearrangements A. Hydrogen-Shift Rearrangements B. Hydride-Shift Rearrangements V. Representative Fragmentations (Spectra) of Classes of Compounds.......... 344 1. Hydrocarbons A. Saturated Hydrocarbons 1) Straight-Chain Hydrocarbons 2) Branched Hydrocarbons 3) Cyclic Hydrocarbons B. Unsaturated C. Aromatic 2. Alkyl Halides 3. Oxygen-Containing Compounds A. Aliphatic Alcohols B. Aliphatic Ethers C. Aromatic Alcohols D. Cyclic Ethers E. Ketones and Aldehydes F. Aliphatic Acids and Esters G. Aromatic Acids and Esters 4. Nitrogen-Containing Compounds A. Aliphatic Amines B. Aromatic Compounds Containing Atoms of Nitrogen C. Heterocyclic Nitrogen-Containing Compounds D. Nitro Compounds E. Concluding Remarks on the Mass Spectra of Nitrogen-Containing Compounds 5. Multiple Heteroatoms or Heteroatoms and a Double Bond 6. Trimethylsilyl Derivative 7. Determining the Location of Double Bonds VI. Library -
Chemoselectivity for B−O and B−H Bond Cleavage by Pincer-Type
pubs.acs.org/IC Article Chemoselectivity for B−O and B−H Bond Cleavage by Pincer-Type Phosphorus Compounds: Theoretical and Experimental Studies ∥ ∥ Qin Zhu, Penglong Wang, Jun Zhu,* Congqing Zhu,* and Guixiang Zeng* Cite This: Inorg. Chem. 2020, 59, 15636−15645 Read Online ACCESS Metrics & More Article Recommendations *sı Supporting Information ABSTRACT: Selective cleavage of the B−O bond or B−H bond in HBpin can be achieved by adjusting the pincer ligand of a phosphorus(III) compound guided by a combination of theoretical prediction and experimental verification. Theoretical calculations reveal that a pincer- type phosphorus compound with an [ONO]3− ligand reacts with HBpin, leading to cleavage of the stronger B−O bonds (ΔG°⧧ = 23.2 kcal mol−1) rather than the weaker B−H bond (ΔG°⧧ = 26.4 kcal mol−1). A pincer-type phosphorus compound with a [NNN]3− ligand reacts with HBpin, leading to the weaker B−H bond cleavage (ΔG°⧧ = 16.2 kcal mol−1) rather than cleavage of the stronger B−O bond (ΔG°⧧ = 33.0 kcal mol−1). The theoretical prediction for B−O bond cleavage was verified experimentally, and the final products were characterized by NMR, HRMS, and single- crystal X-ray diffraction. The chemoselectivity of B−O bond cleavage was also observed in the presence of B−CorB−B bonds in borane substrates. ■ INTRODUCTION attractive because the boron unit can be easily transformed to The formation and cleavage of chemical bonds are fundamental another functional group and substituted borane compounds − concepts in chemistry. Selective activation or cleavage of have unique applications in Suzuki Miyaura coupling reac- 44−47 − chemical bonds provides a green approach to the synthesis of tions. -
Noncovalent Interactions Involving Microsolvated Networks of Trimethylamine N-Oxide
University of Mississippi eGrove Electronic Theses and Dissertations Graduate School 2014 Noncovalent Interactions Involving Microsolvated Networks Of Trimethylamine N-Oxide Kristina Andrea Cuellar University of Mississippi Follow this and additional works at: https://egrove.olemiss.edu/etd Part of the Physical Chemistry Commons Recommended Citation Cuellar, Kristina Andrea, "Noncovalent Interactions Involving Microsolvated Networks Of Trimethylamine N-Oxide" (2014). Electronic Theses and Dissertations. 407. https://egrove.olemiss.edu/etd/407 This Thesis is brought to you for free and open access by the Graduate School at eGrove. It has been accepted for inclusion in Electronic Theses and Dissertations by an authorized administrator of eGrove. For more information, please contact [email protected]. NONCOVALENT INTERACTIONS INVOLVING MICROSOLVATED NETWORKS OF TRIMETHYLAMINE N-OXIDE Kristina A. Cuellar A thesis submitted in partial fulfillment of the requirements for the degree of Master of Science Physical Chemistry University of Mississippi August 2014 Copyright © 2014 Kristina A. Cuellar All rights reserved. ABSTRACT This thesis research focuses on the effects of the formation of hydrogen-bonded networks with the important osmolyte trimethylamine N-oxide (TMAO). Vibrational spectroscopy, in this case Raman spectroscopy, is used to interpret the effects of noncovalent interactions by solvation with select hydrogen bond donors such as water, methanol, ethanol and ethylene glycol in the form of slight changes in vibrational frequencies. Spectral shifts in the experimental Raman spectra of interacting molecules are compared to the results of electronic structure calculations on explicit hydrogen bonded molecular clusters. The similarities in the Raman spectra of microsolvated TMAO using a variety of hydrogen bond donors suggest a common structural motif in all of the hydrogen bonded complexes. -
The Chemistry Induced by Mechanical Load
The chemistry induced by mechanical load Irmgard Frank, Institut für Physikalische Chemie und Elektrochemie, Universität Hannover, Callinstr. 3A, Hannover Abstract Results in the field of mechanochemistry are summarized. For example under mechanical load often a solvolysis is observed instead of a simple homolytic bond rupture. Also a mechanically induced redox reaction was reported experimentally and could be modelled theoretically. With CPMD simulations it is possible to understand multi-step mechanisms in full detail. Introduction The term mechanochemistry started to become fashionable again about 15 years ago. Let me give a personal view of these past 15 years, summarizing and explaining from a distance some of our own papers. Mechanochemistry has an older story in the context of expressions like sonochemistry or tribochemistry. Originally the term mechanochemistry denoted the chemistry observed when solids are heavily grinded in a mortar. The renewed interest stems from the efforts of Hermann Gaub in Munich. He claimed he had measured the force necessary to break a covalent chemical bond, using a scanning tunneling microscope (STM). Results are in the region of 1 – 2 Nanonewton [1]. Just imagine to do that for a strand of a spider web, and then, way smaller, for a single covalent bond! Breaking a single covalent bond within a polymer is certainly easy with any apparatus, but keeping it between the tip of a STM cantilever and a surface in a well-defined state, till the force is measured requires some art of experimentation. Fig. 1: Experimental setup: A polymer fixed between the tip of a cantilever and a surface. Results and Discussion Is it really possible to control a single molecule like this? Starting from 1998, we tried to understand these experiments using mainly Car-Parrinello molecular dynamics (CPMD) simulations. -
Hydrogen Bond
HYDROGEN BOND Hydrogen bond is not a real bond, actually it is a type of electrostatic attraction. It plays very important role in the case of water. So let’s learn more about it with the example of water molecule. You have studied bonding and hybridization of H2O molecule. H2O is a bent shaped molecule. There is a considerable electronegativity difference between H and O atoms which makes the H-O bond polar. More electronegative O pulls bonding pair of electrons and acquires a partial negative charge while Hydrogen develops a partial positive charge. When two molecules of water come closer, the electrostatic force comes in action. Partially negative charged Oxygen of one molecule attracts partially positive charged Hydrogen of another molecule by electrostatic attraction. Electron rich Oxygen shares its lone pair of electron with electron deficient Hydrogen atom and forms an invisible bond of attraction which is called Hydrogen bond. This electrostatic attraction isn’t sufficiently strong to form an ionic bond and the electrons are not shared enough to make it a coordinate covalent bond, but this attraction is somehow capable of keeping the molecules together. Hydrogen bond is represented by a dotted line. It is weaker than ionic and covalent bond. But it is solely responsible for the amazing nature of water. Let’s see how it makes water so wonderful. Hydrogen bonds make a network of water molecules which is responsible for the liquid state of water. When we try to evaporate water into vapours, we need to break a large number of hydrogen bonds to let water molecule free from the network.