Classification of So-Called Non-Covalent Interactions Based
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Noncovalent Bonds Through Sigma and Pi-Hole Located on the Same Molecule. Guiding Principles and Comparisons
molecules Review Noncovalent Bonds through Sigma and Pi-Hole Located on the Same Molecule. Guiding Principles and Comparisons Wiktor Zierkiewicz 1,* , Mariusz Michalczyk 1,* and Steve Scheiner 2 1 Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeze˙ Wyspia´nskiego27, 50-370 Wrocław, Poland 2 Department of Chemistry and Biochemistry, Utah State University Logan, Logan, UT 84322-0300, USA; [email protected] * Correspondence: [email protected] (W.Z.); [email protected] (M.M.) Abstract: Over the last years, scientific interest in noncovalent interactions based on the presence of electron-depleted regions called σ-holes or π-holes has markedly accelerated. Their high directionality and strength, comparable to hydrogen bonds, has been documented in many fields of modern chemistry. The current review gathers and digests recent results concerning these bonds, with a focus on those systems where both σ and π-holes are present on the same molecule. The underlying principles guiding the bonding in both sorts of interactions are discussed, and the trends that emerge from recent work offer a guide as to how one might design systems that allow multiple noncovalent bonds to occur simultaneously, or that prefer one bond type over another. Keywords: molecular electrostatic potential; halogen bond; pnicogen bond; tetrel bond; chalcogen bond; cooperativity Citation: Zierkiewicz, W.; Michalczyk, M.; Scheiner, S. Noncovalent Bonds through Sigma and Pi-Hole Located on the Same 1. Introduction Molecule. Guiding Principles and The concept of the σ-hole, introduced to a wide audience in 2005 at a conference in Comparisons. Molecules 2021, 26, Prague by Tim Clark [1], influenced a way of thinking about noncovalent interactions 1740. -
Preparation and Characterization of Iridium Hydride and Dihydrogen Complexes Relevant to Biomass Deoxygenation
Preparation and Characterization of Iridium Hydride and Dihydrogen Complexes Relevant to Biomass Deoxygenation Jonathan M. Goldberg A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy University of Washington 2017 Reading Committee: D. Michael Heinekey, Chair Karen I. Goldberg, Chair Brandi M. Cossairt Program Authorized to Offer Degree: Department of Chemistry © Copyright 2017 Jonathan M. Goldberg University of Washington Abstract Preparation and Characterization of Iridium Hydride and Dihydrogen Complexes Relevant to Biomass Deoxygenation Jonathan M. Goldberg Chairs of the Supervisory Committee: Professor D. Michael Heinekey Professor Karen I. Goldberg Department of Chemistry This thesis describes the fundamental organometallic reactivity of iridium pincer complexes and their applications to glycerol deoxygenation catalysis. These investigations provide support for each step of a previously proposed glycerol deoxygenation mechanism. Chapter 1 outlines the motivations for this work, specifically the goal of using biomass as a chemical feedstock over more common petroleum-based sources. A discussion of the importance of transforming glycerol to higher value products, such as 1,3-propanediol, is discussed. Chapter 2 describes investigations into the importance of pincer ligand steric factors on the coordination chemistry of the iridium metal center. Full characterization of a five-coordinate iridium-hydride complex is presented; this species was previously proposed to be a catalyst resting state for glycerol deoxygenation. Chapter 3 investigates hydrogen addition to R4(POCOP)Ir(CO) R4 3 t i R4 R4 3 [ POCOP = κ -C6H3-2,6-(OPR2)2 for R = Bu, Pr] and (PCP)Ir(CO) [ (PCP) = κ -C6H3-2,6- t i (CH2PR2)2 for R = Bu, Pr] to give cis- and/or trans-dihydride complexes. -
Application of Aluminium Oxide Nanoparticles to Enhance Rheological and Filtration Properties of Water Based Muds at HPHT Condit
Application of Aluminium Oxide Nanoparticles to Enhance Rheological and Filtration Properties of Water Based Muds at HPHT Conditions Sean Robert Smith1, Roozbeh Rafati*1, Amin Sharifi Haddad1, Ashleigh Cooper2, Hossein Hamidi1 1School of Engineering, University of Aberdeen, Aberdeen, United Kingdom, AB24 3UE 2Baroid Drilling Fluid Laboratory, Halliburton, Dyce, Aberdeen, United Kingdom, AB21 0GN Abstract Drilling fluid is of one of the most important elements of any drilling operation, and through ever advancing technologies for deep water and extended reach drillings, enhancement of drilling fluids properties for such harsh conditions need to be investigated. Currently oil based fluids are used in these types of advanced drilling operations, as their performance at high pressure and high temperature conditions, and deviated wells are superior compared to water based fluids. However, the high costs associated with using them, and environmental concerns of such oil base fluids are drawbacks of them at the moment. In this study, we tried to find a solution for such issues through investigation on the potential application of a new nano-enhanced water base fluid for advanced drilling operations. We analysed the performance of water base drilling fluids that were formulated with two type of nanomaterials (aluminium oxide and silica) at both high and low pressure and temperature conditions (high: up to 120 oC and 500 psi, low: 23 oC and 14.7 psi). The results were compared with a base case drilling fluid with no nanomaterial, and they showed that there is an optimum concentration for aluminium oxide nanoparticles that can be used to improve the rheological and filtration properties of drilling fluids. -
The Hydrogen Bond: a Hundred Years and Counting
J. Indian Inst. Sci. A Multidisciplinary Reviews Journal ISSN: 0970-4140 Coden-JIISAD © Indian Institute of Science 2019. The Hydrogen Bond: A Hundred Years and Counting Steve Scheiner* REVIEW REVIEW ARTICLE Abstract | Since its original inception, a great deal has been learned about the nature, properties, and applications of the H-bond. This review summarizes some of the unexpected paths that inquiry into this phenom- enon has taken researchers. The transfer of the bridging proton from one molecule to another can occur not only in the ground electronic state, but also in various excited states. Study of the latter process has devel- oped insights into the relationships between the nature of the state, the strength of the H-bond, and the height of the transfer barrier. The enormous broadening of the range of atoms that can act as both pro- ton donor and acceptor has led to the concept of the CH O HB, whose ··· properties are of immense importance in biomolecular structure and function. The idea that the central bridging proton can be replaced by any of various electronegative atoms has fostered the rapidly growing exploration of related noncovalent bonds that include halogen, chalco- gen, pnicogen, and tetrel bonds. Keywords: Halogen bond, Chalcogen bond, Pnicogen bond, Tetrel bond, Excited-state proton transfer, CH O H-bond ··· 1 Introduction charge on the proton. The latter can thus attract Over the course of its century of study following the partial negative charge of an approaching its earliest conceptual formulation1,2, the hydro- nucleophile D. Another important factor resides gen bond (HB) has surrendered many of the in the perturbation of the electronic structure mysteries of its source of stability and its myriad of the two species as they approach one another. -
Physical-Chemical Properties of Complex Natural Fluids
Physical-chemical properties of complex natural fluids Vorgelegt von Diplom-Geochemiker Diplom-Mathematiker Sergey Churakov aus Moskau an der Fakultät VI - Bauingenieurwesen und Angewandte Geowissenschaften - der Technischen Universität Berlin zur Erlangung des akademischen Grades Doktor der Naturwissenschaften - Dr. rer. nat. - genehmigte Dissertation Berichter: Prof. Dr. G. Franz Berichter: Prof. Dr. T. M. Seward Berichter: PD. Dr. M. Gottschalk Tag der wissenschaftlichen Aussprache: 27. August 2001 Berlin 2001 D83 Abstract The dissertation is focused on the processes of transport and precipitation of metals in high temperature fumarole gases (a); thermodynamic properties of metamorphic fluids at high pressures (b); and the extent of hydrogen-bonding in supercritical water over wide range of densities and temperatures (c). (a) At about 10 Mpa, degassing of magmas is accompanied by formation of neary ‘dry’ salt melts as a second fluid phase, very strong fractionation of hydrolysis products between vapour and melts, as well as subvalence state of metals during transport processes. Based on chemical analyses of gases and condensates from high-temperature fumaroles of the Kudryavy volcano (i Iturup, Kuril Arc, Russia), a thermodynamic simulation of transport and deposition of ore- and rock-forming elements in high-temperature volcanic gases within the temperature range of 373-1373 K at 1 bar pressure have been performed. The results of the numerical simulations are consistent with field observations. Alkali and alkali earth metals, Ga, In, Tl, Fe, Co, Ni, Cu, and Zn are mainly transported as chlorides in the gas phase. Sulfide and chloride forms are characteristic of Ge, Sn, Pb, and Bi at intermediate and low temperatures. -
Impact of Solute Molecular Properties on the Organization of Nearby Water: a Cellular Automata Model
Digest Journal of Nanomaterials and Biostructures Vol. 7, No. 2, April - June 2012, p. 469 - 475 IMPACT OF SOLUTE MOLECULAR PROPERTIES ON THE ORGANIZATION OF NEARBY WATER: A CELLULAR AUTOMATA MODEL C. MIHAIa, A. VELEAb,e, N. ROMANc, L. TUGULEAa, N. I. MOLDOVANd** aDepartment of Electricity, Solid State and Biophysics, Faculty of Physics, University of Bucharest, Romania bNational Institute of Materials Physics, Bucharest - Magurele, Romania cDepartment of Computer Science, The Ohio State University - Lima, Ohio, USA dDepartment of Internal Medicine, Davis Heart and Lung Research Institute, The Ohio State University - Columbus, Ohio, USA e"Horia Hulubei” Foundation, Bucharest-Magurele, Romania The goal of this study was the creation of a model to understand how solute properties influence the structure of nearby water. To this end, we used a two-dimensional cellular automaton model of aqueous solutions. The probabilities of translocation of water and solute molecules to occupy nearby sites, and their momentary distributions (including that of vacancies), are considered indicative of solute molecular mechanics and hydrophatic character, and are reflected in water molecules packing, i.e. ‘organization’. We found that in the presence of hydrophilic solutes the fraction of water molecules with fewer neighbors was dominant, and inverse-proportionally dependent on their relative concentration. Hydrophobic molecules induced water organization, but this effect was countered by their own flexibility. These results show the emergence of cooperative effects in the manner the molecular milieu affects local organization of water, and suggests a mechanism through which molecular mechanics and crowding add a defining contribution to the way the solute impacts on nearby water. -
Chemical Physics 524 (2019) 55–62
Chemical Physics 524 (2019) 55–62 Contents lists available at ScienceDirect Chemical Physics journal homepage: www.elsevier.com/locate/chemphys Structures of clusters surrounding ions stabilized by hydrogen, halogen, T chalcogen, and pnicogen bonds ⁎ ⁎ Steve Scheinera, , Mariusz Michalczykb, Wiktor Zierkiewiczb, a Department of Chemistry and Biochemistry, Utah State University Logan, Utah 84322-0300, United States b Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland ARTICLE INFO ABSTRACT Keywords: Four H-binding HCl and HF molecules position themselves at the vertices of a tetrahedron when surrounding a Tetrahedral central Cl−. Halogen bonding BrF and ClF form a slightly distorted tetrahedron, a tendency that is amplified for QTAIM ClCN which forms a trigonal pyramid. Chalcogen bonding SF2, SeF2, SeFMe, and SeCSe occupy one hemisphere NBO of the central ion, leaving the other hemisphere empty. This pattern is repeated for pnicogen bonding PF3, SeF3 Cl− and AsCF. The clustering of solvent molecules on one side of the Cl− is attributed to weak attractive interactions Na+ between them, including chalcogen, pnicogen, halogen, and hydrogen bonds. Binding energies of four solvent molecules around a central Na+ are considerably reduced relative to chloride, and the geometries are different, with no empty hemisphere. The driving force maximizes the number of electronegative (F or O) atoms close to the Na+, and the presence of noncovalent bonds between solvent molecules. 1. Introduction particular, the S, Se, etc group can engage in chalcogen bonds (YBs) [19–25], and the same is true of the P, As family which forms pnicogen The hydrogen bond (HB) is arguably the most important and in- bonds (ZBs) [26–34]. -
Quantitative Analysis of Hydrogen and Chalcogen Bonds in Two Pyrimidine
Zurich Open Repository and Archive University of Zurich Main Library Strickhofstrasse 39 CH-8057 Zurich www.zora.uzh.ch Year: 2020 Quantitative analysis of hydrogen and chalcogen bonds in two pyrimidine-5-carbonitrile derivatives, potential DHFR inhibitors: an integrated crystallographic and theoretical study Al-Wahaibi, Lamya H ; Chakraborty, Kushumita ; Al-Shaalan, Nora H ; Syed Majeed, Mohamed Yehya Annavi ; Blacque, Olivier ; Al-Mutairi, Aamal A ; El-Emam, Ali A ; Percino, M Judith ; Thamotharan, Subbiah Abstract: Two potential bioactive pyrimidine-5-carbonitrile derivatives have been synthesized and char- acterized by spectroscopic techniques (1H and 13C-NMR) and the three dimensional structures were elucidated by single crystal X-ray diffraction at low temperature (160 K). In both structures, the molec- ular conformation is locked by an intramolecular C–HC interaction involving the cyano and CH of the thiophene and phenyl rings. The intermolecular interactions were analyzed in a qualitative man- ner based on the Hirshfeld surface and 2D-fingerprint plots. The results suggest that the phenyl and thiophene moieties have an effect on the crystal packing. For instance, the chalcogen bonds areonly preferred in the thiophene derivative. However, both structures uses a common N–HO hydrogen bond motif. Moreover, the structures of 1 and 2 display 1D isostructurality and molecular chains stabilize by intermolecular N–HO and N–HN hydrogen bonds. The nature and extent of different non-covalent interactions were further characterized by the topological parameters derived from the quantum the- ory of atoms-in-molecules approach. This analysis indicates that apart from N–HO hydrogen bonds, other non-covalent interactions are closed-shell in nature. -
Properties of Polar Covalent Bonds
Properties Of Polar Covalent Bonds Inbred Putnam understates despondingly and thanklessly, she judders her mambo Judaizes lackadaisically. Ish and sealed Mel jazz her Flavia stull unhasp and adsorb pugnaciously. Comtist and compartmental Kirk regularizes some sims so gutturally! Electronegativity form is generated by a net positve charge, not symmetrical and some of polar covalent bond is nonpolar covalent bond polarity That results from the sharing of valence electrons is a covalent bond from a covalent bond the. These negatively charged ions form. Covalent bond in chemistry the interatomic linkage that results from the. Such a covalent bond is polar and cream have a dipole one heir is positive and the. Chemistry-polar and non-polar molecules Dynamic Science. Chapter 1 Structure Determines Properties Ch 1 contents. Properties of polar covalent bond always occurs between different atoms electronegativity difference between bonded atoms is moderate 05 and 19 Pauling. Covalent character of a slight positive charge, low vapour pressure, the molecules align themselves away from their valence shell of electrons! What fee the properties of a polar molecule? Polar bonds form first two bonded atoms share electrons unequally. Has a direct latch on many properties of organic compounds like solubility boiling. Polar covalent bond property, causing some properties of proteins and each? When trying to bond property of properties are stuck together shifts are shared. Covalent bonds extend its all directions in the crystal structure Diamond tribute one transparent substance that peddle a 3D covalent network lattice. Acids are important compounds with specific properties that turnover be dis- cussed at burn in. -
Synthesis and Investigation of the Properties of Water Soluble Quantum Dots for Bioapplications
Synthesis and Investigation of the Properties of Water Soluble Quantum Dots for Bioapplications A Thesis by Fatemeh Mir Najafi Zadeh Submitted in Partial Fulfilment of the Recruitment for the Degree of Doctor of Philosophy in Chemistry Supervisor: A/Prof. John A.Stride Co-supervisor: A/Prof. Marcus Cole School of Chemistry Faculty of Science August 2014 The University of New South Wales Thesis/ Dissertation Sheet Surname or family name: Mir Najafi Zadeh First name: Fatemeh Other name/s: Abbreviation for degree as given in the University calendar: PhD School: Chemistry Faculty: Science Title: Synthesis and Investigation of the Properties of Water Soluble Quantum Dots for Bioapplications Abstract Semiconductor nanocrystals or quantum dots (QDs) have received a great deal of attention over the last decade due to their unique optical and physical properties, classifying them as potential tools for biological and medical applications. However, there are some serious restrictions to the bioapplications of QDs such as water solubility, toxicity and photostability in biological environments for both in-vivo and in-vitro studies. In this thesis, studies have focused on the preparation of highly luminescent, water soluble and photostable QDs of low toxicity that can then be potentially used in a biological context. First, CdSe nanoparticles were synthesized in an aqueous route in order to investigate the parameters affecting formation of nanoparticles. Then, water soluble CdSe(S) and ZnSe(S) QDs were synthesized. These CdSe(S) QDs were also coated with ZnO and Fe2O3 to produce CdSe(S)/ZnO and CdSe(S)/Fe2O3 core/shell QDs. The cytotoxicities of as-prepared CdSe(S), ZnSe (S) and CdSe(S)/ZnO QDs were studied in the presence of two cell lines: HCT-116 cell line as cancer cells and WS1 cell line as normal cells. -
The Water Molecule
Seawater Chemistry: Key Ideas Water is a polar molecule with the remarkable ability to dissolve more substances than any other natural solvent. Salinity is the measure of dissolved inorganic solids in water. The most abundant ions dissolved in seawater are chloride, sodium, sulfate, and magnesium. The ocean is in steady state (approx. equilibrium). Water density is greatly affected by temperature and salinity Light and sound travel differently in water than they do in air. Oxygen and carbon dioxide are the most important dissolved gases. 1 The Water Molecule Water is a polar molecule with a positive and a negative side. 2 1 Water Molecule Asymmetry of a water molecule and distribution of electrons result in a dipole structure with the oxygen end of the molecule negatively charged and the hydrogen end of the molecule positively charged. 3 The Water Molecule Dipole structure of water molecule produces an electrostatic bond (hydrogen bond) between water molecules. Hydrogen bonds form when the positive end of one water molecule bonds to the negative end of another water molecule. 4 2 Figure 4.1 5 The Dissolving Power of Water As solid sodium chloride dissolves, the positive and negative ions are attracted to the positive and negative ends of the polar water molecules. 6 3 Formation of Hydrated Ions Water dissolves salts by surrounding the atoms in the salt crystal and neutralizing the ionic bond holding the atoms together. 7 Important Property of Water: Heat Capacity Amount of heat to raise T of 1 g by 1oC Water has high heat capacity - 1 calorie Rocks and minerals have low HC ~ 0.2 cal. -
Binuclear Copper(I) Borohydride Complex Containing Bridging Bis
crystals Article Binuclear Copper(I) Borohydride Complex Containing Bridging Bis(diphenylphosphino) Methane Ligands: Polymorphic Structures of 2 [(µ2-dppm)2Cu2(η -BH4)2] Dichloromethane Solvate Natalia V. Belkova 1 ID , Igor E. Golub 1,2 ID , Evgenii I. Gutsul 1, Konstantin A. Lyssenko 1, Alexander S. Peregudov 1, Viktor D. Makhaev 3, Oleg A. Filippov 1 ID , Lina M. Epstein 1, Andrea Rossin 4 ID , Maurizio Peruzzini 4 and Elena S. Shubina 1,* ID 1 A. N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences (INEOS RAS), 119991 Moscow, Russia; [email protected] (N.V.B.); [email protected] (I.E.G.); [email protected] (E.I.G.); [email protected] (K.A.L.); [email protected] (A.S.P.); [email protected] (O.A.F.); [email protected] (L.M.E.) 2 Inorganic Chemistry Department, Peoples’ Friendship University of Russia (RUDN University), 117198 Moscow, Russia 3 Institute of Problems of Chemical Physics, Russian Academy of Sciences (IPCP RAS), 142432 Moscow, Russia; [email protected] 4 Istituto di Chimica dei Composti Organometallici Consiglio Nazionale delle Ricerche (ICCOM CNR), 50019 Sesto Fiorentino, Italy; [email protected] (A.R.); [email protected] (M.P.) * Correspondence: [email protected]; Tel.: +7-495-135-5085 Academic Editor: Sławomir J. Grabowski Received: 18 September 2017; Accepted: 17 October 2017; Published: 20 October 2017 Abstract: Bis(diphenylphosphino)methane copper(I) tetrahydroborate was synthesized by ligands exchange in bis(triphenylphosphine) copper(I) tetrahydroborate, and characterized by XRD, FTIR, NMR spectroscopy. According to XRD the title compound has dimeric structure, [(µ2-dppm)2Cu2(η2-BH4)2], and crystallizes as CH2Cl2 solvate in two polymorphic forms (orthorhombic, 1, and monoclinic, 2) The details of molecular geometry and the crystal-packing pattern in polymorphs were studied.