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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# -
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. -
Structure and Bonding of New Boron and Carbon Superpolyhedra
Structural Chemistry (2019) 30:805–814 https://doi.org/10.1007/s11224-019-1279-5 ORIGINAL RESEARCH Structure and bonding of new boron and carbon superpolyhedra Olga A. Gapurenko1 & Ruslan M. Minyaev1 & Nikita S. Fedik2 & Vitaliy V. Koval1 & Alexander I. Boldyrev2 & Vladimir I. Minkin1 Received: 16 November 2018 /Accepted: 1 January 2019 /Published online: 10 January 2019 # Springer Science+Business Media, LLC, part of Springer Nature 2019 Abstract Using the DFT methods, we computationally predict the stability of cage compounds E4nRn (E = B, C; R = H, F; n = 4, 8, 12, 24) based on Platonic bodies and Archimedean polyhedrons in which all vertices are replaced by tetrahedral E4R fragments. Cage compounds B60R12 and C60 with pyramidal units B5RorC5 are also examined and it is shown that only boron compounds are stable. The nature of chemical bonding in the discussed compounds is analyzed using the AdNDP and NBO methods. The hydrocarbons have classical 2c-2e C-C σ-bonds, while the boron compounds are formed by the polyhedral units with the delocalized multicenter bonds which connected three and more boron atoms. The new example of spherical aromaticity accord- 2 ing to the 2(N+1) rule in the case of B16F4 with multicenter 16c-2e bonds are revealed. Stable compound B60H12 contains 12 5c- 2e B-B bonds. Keywords Сage clusters . Chemical bonding . 3c-2e bond . Spherical aromaticity . AdNDP . NBO Construction of novel allotropic forms of carbon based on was proposed [1] as the system with the same symmetry as the tetrahedrane- and cubane-like building blocks was pro- sp3-carbon to replace the carbon atoms in the diamond posed by Burdett and Lee [1] and by Johnston and lattice. -
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. -
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. -
Ring-Opening Alkyne Metathesis Methods for Functional Conjugated Polymer Synthesis by Stephen W. Von Kugelgen a Dissertation
Ring-Opening Alkyne Metathesis Methods For Functional Conjugated Polymer Synthesis by Stephen W. von Kugelgen A dissertation submitted in partial satisfaction of the requirements for the degree of Doctor of Philosophy in Chemistry in the Graduate Division of the University of California, Berkeley Committee in charge: Professor Felix R. Fischer, Chair Professor Robert G. Bergman Professor Phillip B. Messersmith Fall 2018 Ring-Opening Alkyne Metathesis Methods For Functional Conjugated Polymer Synthesis Copyright 2018 by Stephen W. von Kugelgen 1 Abstract Ring-Opening Alkyne Metathesis Methods For Functional Conjugated Polymer Synthesis by Stephen W. von Kugelgen Doctor of Philosophy in Chemistry University of California, Berkeley Professor Felix R. Fischer, Chair Since its discovery in the mid 20th century, most applications of alkyne metathesis have relied on thermodynamics to control product distributions. Ring-opening alkyne metathe- sis polymerization (ROAMP), in contrast, requires the kinetic product of metathesis of a strained, cyclic alkyne monomer to give a living, chain-growth polymerization (Chapter 1, Introduction). This living polymerization of conjugated alkyne-containing monomers has the potential to access a wide range of functional poly(arylene ethynylene) materials with excep- tional control over length, dispersity, topology, and endgroups. To this end, we demonstrate the first ROAMP synthesis of conjugated poly(ortho-phenylene ethynylene) and elucidate a mechanistic description of the reaction to understand the enabling catalyst selectivity and unexpectely find that initiator sterics dictate endgroup fidelity and polymer topology (Chap- ter 2). To disentangle the role of steric and electronic factors in initiator performance, we describe a novel synthetic method that gives a series of isosteric benzylidyne catalysts which exhibit a strong, deterministic electronic effect on both ROAMP initiation rates and polymer endgroup fidelity (Chapter 3). -
Non-Covalent Short Range Interactions
WORKSHOP Nanoscience on the Tip Non-Covalent Short Range Interactions Table of Contents: 1. Motivation ............................................................................................................ 1 2. Short Range Interactions and Surface Forces ...................................................... 1 3. Van der Waals Interactions for Point Interactions ............................................... 3 4. Surface Forces...................................................................................................... 4 5. Hamaker Constant................................................................................................ 5 6. Van der Waals Retardation Effects ...................................................................... 6 7. Adhesion and Surface Energies............................................................................ 6 8. Cutoff Distance for Van der Waals Calculations................................................. 7 9. Capillary Forces due to Vapor Condensation ...................................................... 8 10. Critical Humidity for Capillary Neck Formation................................................. 9 11. Estimation of the Tip Radius Utilizing the Capillary Effects ............................10 12. Modification of Hydrophobicity (Wettability)................................................... 12 13. Force Displacement Curves ............................................................................... 13 References ................................................................................................................ -
Interplay of Ring Puckering and Hydrogen Bonding In
Article Cite This: J. Phys. Chem. A 2019, 123, 7087−7103 pubs.acs.org/JPCA Interplay of Ring Puckering and Hydrogen Bonding in Deoxyribonucleosides Published as part of The Journal of Physical Chemistry virtual special issue “Leo Radom Festschrift”. ‡ ‡ Siying Lyu, Nassim Beiranvand, Marek Freindorf, and Elfi Kraka* Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Ave, Dallas, Texas 75275-0314, United States *S Supporting Information ABSTRACT: The Cremer−Pople ring puckering analysis and the Konkoli−Cremer local mode analysis supported by the topological analysis of the electron density were applied for the first comprehensive analysis of the interplay between deoxy- ribose ring puckering and intramolecular H-bonding in 2′- deoxycytidine, 2′-deoxyadenosine, 2′-deoxythymidine, and 2′- deoxyguanosine. We mapped for each deoxyribonucleoside the complete conformational energy surface and the corresponding pseudorotation path. We found only incomplete pseudorotation cycles, caused by ring inversion, which we coined as pseudolibration paths. On each pseudolibration path a global and a local minimum separated by a transition state were identified. The investigation of H-bond free deoxyribonucleo- side analogs revealed that removal of the H-bond does not restore the full conformational flexibility of the sugar ring. Our work showed that ring puckering predominantly determines the conformational energy; the larger the puckering amplitude, the lower the conformational energy. In contrast no direct correlation between conformational energy and H-bond strength was found. The longest and weakest H-bonds are located in the local minimum region, whereas the shortest and strongest H-bonds are located outside the global and local minimum regions at the turning points of the pseudolibration paths, i.e., H-bonding determines the shape and length of the pseudolibration paths. -
Transition Metal Activation and Functionalization of Carbon-Hydrogen Bonds
FINAL REPORT SUBMITTED TO THE DEPARTMENT OF ENERGY BY University of Rochester River Campus Rochester, New York 14627 FOR TRANSITION METAL ACTIVATION AND FUNCTIONALIZATION OF CARBON-HYDROGEN BONDS William D. Jones, Principal Investigator Phone: 716-275-5493 Contract No. DE-FG02-86ER13569 Project Period: December 1, 1998 - November 30, 2001 Total Award Amount (3 years): $ 396,000 Unexpended Balance at End of Grant Period: $0 DOE Report, 1998-2001 2 William D. Jones Overview of Research Accomplishments for the Period Dec. 1, 1998-Nov. 30, 2001: These past 3 years, our research has focussed on the items presented in our proposal where we have had success. These include: (1) carbon-carbon bond cleavage reactions, (2) fundamental studies of C-H bond cleavage reactions of trispyrazolylboraterhodium complexes, (3) catalytic C-H and C-C bond functionalization, and (4) carbon-fluorine bond activation. We have made progress in each of these areas, as described in the following report, and will continue our studies in these areas. Our carbon-carbon bond cleavage study is based upon the notion that metal-phenyl bonds are the strongest metal-carbon bonds. Cleavage of the C-C bonds in biaryl systems will therefore give two very strong metal-aryl bonds, and consequently offers the most thermodynamically preferred situation for observing C-C cleavage. We have had extensive success in C-C cleavage with biphenylene, a molecule with a weaker C-C bond than biphenyl. The success includes not only several new nickel, palladium, and platinum based metal systems of the type [M(chelating phosphine)] but also related rhodium systems for C-C cleavage. -
Electrostatic Potential Topology for Probing Molecular Structure, Bonding and Reactivity
molecules Review Electrostatic Potential Topology for Probing Molecular Structure, Bonding and Reactivity Shridhar R. Gadre 1,* , Cherumuttathu H. Suresh 2,* and Neetha Mohan 2 1 Department of Chemistry, Interdisciplinary School of Scientific Computing, Savitribai Phule University, Pune 411007, India 2 Chemical Sciences and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Trivandrum 695019, India; [email protected] * Correspondence: [email protected] (S.R.G.); [email protected] (C.H.S.) Abstract: Following the pioneering investigations of Bader on the topology of molecular electron density, the topology analysis of its sister field viz. molecular electrostatic potential (MESP) was taken up by the authors’ groups. Through these studies, MESP topology emerged as a powerful tool for exploring molecular bonding and reactivity patterns. The MESP topology features are mapped in terms of its critical points (CPs), such as bond critical points (BCPs), while the minima identify electron-rich locations, such as lone pairs and π-bonds. The gradient paths of MESP vividly bring out the atoms-in-molecule picture of neutral molecules and anions. The MESP-based characterization of a molecule in terms of electron-rich and -deficient regions provides a robust prediction about its interaction with other molecules. This leads to a clear picture of molecular aggregation, hydrogen bonding, lone pair–π interactions, π-conjugation, aromaticity and reaction mechanisms. This review summarizes the contributions of the authors’ groups over the last three decades and those of the Citation: Gadre, S.R.; Suresh, C.H.; other active groups towards understanding chemical bonding, molecular recognition, and reactivity Mohan, N. Electrostatic Potential through topology analysis of MESP. -
Alkyne-Cobalt-Clusters
COBALT -CLUSTER MEDIATED PROPARGYL CATION AND RADICAI.J REARRANGEMENTS ALKYNE-COBALT-CLUSTERS: SYNTHESES, STRUCTURES AND REARRANGEMENTS OF METAL··STABILIZED PROPARGYL CATIONS AND RADICALS By JOHN H. KALDIS, B.Sc. A Thesis Submitted to the School of Graduate Studies In Partial Fulfillment ofthe Requirements for the Degree Doctor of Philosophy McMaster University © Copyright by John H. Kaldis, August 2003 DOCTOR OF PHILOSOPHY (2003) McMaster University (Chemistry) Hamilton, Ontario TITLE: Alkyne-Cobalt-Clusters: Syntheses, Structures and Rearrangements of Metal-Stabilized Propargyl Cations and Radicals AUTHOR: John H. Kaldis, B.Sc. (University of Western Ontario) SUPERVISOR: Dr. Michael J. McGlinchey NUMBER OF PAGES: XV, 192 11 Abstract Cobalt-clusters are versatile reagents in organometallic chemistry. Their ability to protect an alkyne allows one to selectively manipulate a ligand without undergoing a competitive reaction from the alkyne. Cobalt-clusters geometrically modify linear alkynes to 136-145° degrees, thereby allowing for some non-traditional alkynyl chemistry to occur. In particular, the focus of this dissertation lies upon the chemistry of cobalt-complexed propargyl alkynols, the ability of cobalt to stabilize neighbouring cations generated from these alcohols, and the chemistry that can be accomplished by altering the steric and electronic effects. We have chosen to study the possibility of inducing migration of various substituents from one terminus of the cobalt-complexed alkyne to the alcoholic site ofthe propargyl group via protonation ofthe desired complex. While examining various silanes, and altering the propargyl alcohol itself, we have considered both steric and electronic effects, thereby determining the idealized conditions for such transfers to occur. Furthermore, in our attempts to successfully apply these migrations to several systems, we have acquired a diverse synthetic knowledge of propargyl cobalt-clusters and their intricate reactivity.