Quantum Crystallography: Current Developments and Future
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Ins#Tute for Advanced Computa#Onal Science
Instute for Advanced Computaonal Science Robert J. Harrison, Director [email protected] 1 What is IACS? • A muldisciplinary instute with a focus on computaonal and data science • $20M endowment to support 3 endowed chairs and operaons (~$13M) • 12 core faculty, 32 affiliate faculty, 100+ students with plans to grow to 16+ core and 150+ students • Newly renovated space – ~6000 sq. ., 17 faculty offices, 45 students • Vision and mission to excel, lead and serve • Educaon and research without walls 2 IACS Organizaonal Chart Vision Our vision is to be an internaonally recognized center in data and computaonal science, having vibrant muldisciplinary research and educaon programs, with broad leadership and benefit across Stony Brook and SUNY, and with demonstrated economic benefit to New York State. 4 IACS Faculty and Community Community • Benefing from our instuonal Community and intellectual leadership, educaon and training, shared resources, and online materials Affiliated Affiliated faculty & students • Collaborators and strategic partners • Have full access to IACS resources and student awards/fellowships Core faculty and students Core • Faculty have 50% appointment in IACS with MOU • Fundamentals and applicaons of computaonal science 5 IACS Core Faculty - I • Alan Calder (astro. phys.) Deputy Director • Barbara Chapman (comp.sci.) • Rezaul Chowdhury (comp. sci.) • Marivi Fernández-Serra (cond. ma.) 6 IACS Core Faculty - II • Robert J. Harrison (chemistry) Director • Predrag KrsBć • Xiangmin Jiao (app. math.) • Marat Khairoutdinov (atmos. sci.) 7 IACS Core Faculty - III • Artem Oganov (materials) • Ma Reuter (math/chem. phys.) • Arnout van de Rijt (sociology) 8 IACS Research Themes Numerics and algorithms: Numerics and Jiao, Chowdhury, Harrison, (all) algorithms Materials and chemistry by design: Producvity Materials and Fernández-Serra, Oganov, KrsBć, and chemistry by Harrison, Reuter performance design Interdisciplinary faculty in Social sciences and humanies: foundaons and van de Rijt (and affiliates) applicaons of computaonal science Physical, env. -
Quantum Crystallography†
Chemical Science View Article Online MINIREVIEW View Journal | View Issue Quantum crystallography† Simon Grabowsky,*a Alessandro Genoni*bc and Hans-Beat Burgi*de Cite this: Chem. Sci.,2017,8,4159 ¨ Approximate wavefunctions can be improved by constraining them to reproduce observations derived from diffraction and scattering experiments. Conversely, charge density models, incorporating electron-density distributions, atomic positions and atomic motion, can be improved by supplementing diffraction Received 16th December 2016 experiments with quantum chemically calculated, tailor-made electron densities (form factors). In both Accepted 3rd March 2017 cases quantum chemistry and diffraction/scattering experiments are combined into a single, integrated DOI: 10.1039/c6sc05504d tool. The development of quantum crystallographic research is reviewed. Some results obtained by rsc.li/chemical-science quantum crystallography illustrate the potential and limitations of this field. 1. Introduction today's organic, inorganic and physical chemistry. These tools are usually employed separately. Diffraction and scattering Quantum chemistry methods and crystal structure determina- experiments provide structures at the atomic scale, while the Creative Commons Attribution 3.0 Unported Licence. tion are highly developed research tools, indispensable in techniques of quantum chemistry provide wavefunctions and aUniversitat¨ Bremen, Fachbereich 2 – Biologie/Chemie, Institut fur¨ Anorganische eUniversitat¨ Zurich,¨ Institut fur¨ Chemie, Winterthurerstrasse 190, CH-8057 Zurich,¨ Chemie und Kristallographie, Leobener Str. NW2, 28359 Bremen, Germany. Switzerland E-mail: [email protected] † Dedicated to Prof. Louis J. Massa on the occasion of his 75th birthday and to bCNRS, Laboratoire SRSMC, UMR 7565, Vandoeuvre-l`es-Nancy, F-54506, France Prof. Dylan Jayatilaka on the occasion of his 50th birthday in recognition of their cUniversit´e de Lorraine, Laboratoire SRSMC, UMR 7565, Vandoeuvre-l`es-Nancy, F- pioneering contributions to the eld of X-ray quantum crystallography. -
X-Ray Diffraction & Elemental Analysis Welcome
X-ray Diff raction & Elemental Analysis Featured Rigaku Journal Article 2 Welcome X-ray thin-fi lm measurement techniques VII. (Pole fi gure All of us who put The Bridge together wish our readers a happy holiday period as we end measurement) one year and begin another. In 2014 we will be adding some interesting new features to The Bridge that should be useful from a training and educational perspective. The AZX400 Sequential 2 This particular issue has a number of articles concerning thin fi lms, both their production WDXRF Spectrometer and their properties. The use of thin fi lms continues to play a big part in the advancement AZX400 Application Report of new materials and The Bridge is committed to highlighting areas involving thin fi lm Analysis of MTJ structures technology in our overall mission of keeping abreast of advances in materials analysis. Featured Application Note 3 Enjoy the newsletter. Chemical Bath for Copper Foil Surface Treatment A bridge is often used to symbolize a connection or link between two places, and thus we felt The Bridge would be the perfect name for our eNewsletter, as we hope that it will act Rigaku Conferences 4 as a vehicle for the transmission of ideas and information between Rigaku and interested readers around the world. Supermini200 Spectrometer 5 BioSAXS-1000 6 Customer in the Spotlight 6 The fi rst BioSAXS-1000, The University of Texas Medical And a bridge is a two-way Branch at Galveston, UTMB structure, a concept that we will keep in mind as we not The Adventures of Captain Nano 7 only provide information about Rigaku, but also report Scientifi c Book Review 8 on interesting research and the associated laboratories Training Classes 9 around the world, publish technical book reviews that might help our readers in Recent Scientifi c 10 Papers of Interest their work, and highlight general news topics that are of interest to many Material Analysis in the News 11 people involved in materials analysis. -
Quantum Reform
feature Quantum reform Leonie Mueck Quantum computers potentially offer a faster way to calculate chemical properties, but the exact implications of this speed-up have only become clear over the last year. The first quantum computers are likely to enable calculations that cannot be performed classically, which might reform quantum chemistry — but we should not expect a revolution. t had been an exhausting day at the 2012 International Congress of Quantum IChemistry with countless presentations reporting faster and more accurate methods for calculating chemical information using computers. In the dry July heat of Boulder, Colorado, a bunch of young researchers decided to end the day with a cool beer, but the scientific discussion didn’t fade away. Thoughts on the pros and cons of all the methods — the approximations they involved and the chemical problems that they could solve — bounced across the table, until somebody said “Anyway, in a few years we will have a quantum computer and our approximate methods will be obsolete”. An eerie silence followed. What a frustrating thought! They were devoting their careers to quantum chemistry — working LIBRARY PHOTO RICHARD KAIL/SCIENCE tirelessly on applying the laws of quantum mechanics to treat complex chemical of them offering a different trade-off between cannot do on a ‘classical’ computer, it does problems with a computer. And in one fell accuracy and computational feasibility. not look like all the conventional quantum- swoop, would all of those efforts be wasted Enter the universal quantum computer. chemical methods will become obsolete or as chemists turn to quantum computers and This dream machine would basically work that quantum chemists will be out of their their enormous computing power? like a normal digital computer; it would jobs in the foreseeable future. -
Title: Unexpected Stable Stoichiometries of Sodium Chlorides
Title: Unexpected stable stoichiometries of sodium chlorides Authors: Weiwei Zhang1, 2, *, Artem R. Oganov2, 3, 4*, Alexander F. Goncharov5,6, Qiang Zhu2, Salah Eddine Boulfelfel2, Andriy O. Lyakhov2, Elissaios Stavrou5, Maddury Somayazulu5, Vitali B. Prakapenka7, Zuzana Konôpková8 Affiliations: 1 Department of Applied Physics, China Agricultural University, Beijing, 100080, China. 2Department of Geosciences, Center for Materials by Design, and Institute for Advanced Computational Science, State University of New York, Stony Brook, NY 11794-2100, U.S.A. 3Moscow Institute of Physics and Technology, 9 Institutskiy Lane, Dolgoprudny city, Moscow Region, 141700, Russia 4School of Materials Science, Northwestern Polytechnical University, Xi'an,710072, China 5Geophysical Laboratory, Carnegie Institution of Washington, 5251 Broad Branch Road NW, Washington, D.C. 20015, U.S.A. 6Center for Energy Matter in Extreme Environments and Key Laboratory of Materials Physics, Institute of Solid State Physics, Chinese Academy of Sciences, 350 Shushanghu Road, Hefei, Anhui 230031, China 7Center for Advanced Radiation Sources, University of Chicago, Chicago, Illinois 60637, U.S.A. 8Photon Science DESY, D-22607 Hamburg, Germany *To whom correspondence should be addressed. E-mail: [email protected], [email protected]. Abstract: Sodium chloride (NaCl), or rocksalt, is well characterized at ambient pressure. Due to the large electronegativity difference between Na and Cl atoms, it has highly ionic chemical bonding, with stoichiometry 1:1 dictated by charge balance, and B1-type crystal structure. Here, by combining theoretical predictions and diamond anvil cell experiments we show that new materials with different stoichiometries emerge at pressure as low as 20 GPa. Compounds such us Na3Cl, Na2Cl, Na3Cl2, NaCl3 and NaCl7 are theoretically stable and have unusual bonding and electronic properties. -
Quantum Chemistry and Spectroscopy – Spring 2018
CHE 336 – Quantum Chemistry and Spectroscopy – Spring 2018 Instructor: Dr. Jessica Sarver Email: [email protected] Office: HSC 364 (email hours: 8 am – 10 pm) Office Hours: 10am-12pm Tuesday, 2-3pm Wednesday, 10:30-11:30am Friday, or by appointment Course Description (from Westminster undergraduate catalog) Quantum chemistry and spectroscopy is the study of the microscopic behavior of matter and its interaction with electromagnetic radiation. Topics include the formulation and application of quantum mechanical models, atomic and molecular structure, and various spectroscopic techniques. Laboratory activities demonstrate the fundamental principles of physical chemistry. Methods that will be used during the laboratory portion include: polarimetry, UV-Vis and fluorescence spectroscopies, electrochemistry, and computational/molecular modeling. Prerequisites: C- grade in CHE 117 and MTH 152 and PHY 152. Course Outcomes The chemistry major outcomes are: • Describe and explain quantum theory and the three quantum mechanical models of motion. • Describe and explain how these theories/models are applied and incorporated to applications of atomic/molecular structure and spectroscopy. • Describe and explain the principles of four major types of spectroscopy and their applications. • Describe and explain the measurable thermodynamic parameters for physical and chemical processes and equilibria. • Describe and explain how chemical kinetics can be used to investigate time-dependent processes. • Solve mathematical problems based on physical chemical principles and connect the numerical results with these principles. Textbook The text for this course is Physical Chemistry, 10th Ed. by Atkins and de Paula. Readings and problem set questions will be assigned from this text. You are strongly urged to get a copy of this textbook and complete all the assigned readings and homework. -
'Forbidden' Chemistry 11 February 2016
Scientists gain insights into 'forbidden' chemistry 11 February 2016 "We showed how the insights gained in the present study can be used to rationalize the stability of recently discovered high-pressure compounds," say the authors in their paper. In a previous experiment, Oganov and his colleagues discovered several 'forbidden' compounds- Na3Cl, NaCl3, NaCl7,and even Na3Cl2. These compounds are only stable under extreme pressure (approximately 200,000 atmospheres) and they decompose under normal conditions on Earth. However, understanding how new compounds become stable under high pressure is of utmost importance for planetary science. The structures of 'textbook' NaCl (left) and 'forbidden' A3Y (A=Li, Na, K; Y= Cl, Br) (right) are shown. Credit: The principle that explains the unusual ratio of Na MIPT press office and Cl atoms in 'forbidden' compounds is that the number of interactions between Na and Cl atoms increases while interactions between sodium atoms break down. Gabriele Saleh, a research fellow at MIPT, and Prof. Artem Oganov, a Laboratory Supervisor at The interactions between neighbouring atoms in a MIPT and Professor at the Skolkovo Institute of crystal are responsible for the structure and Science and Technology (Skoltech), have properties of the crystal (remember carbon and discovered what causes the stability of various graphite). compounds that are not commonly found in 'textbook' chemistry. Upon formation of these 'forbidden compounds', new Na-Cl interactions are formed at the expenses The reorganisation of the chemical interactions of Na-Na metallic bonds. The competition between results in the stability of the 'new' structure of the these two bonding types, influenced by pressure, compounds. -
Complex Chemical Reaction Networks from Heuristics-Aided Quantum Chemistry
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Harvard University - DASH Complex Chemical Reaction Networks from Heuristics-Aided Quantum Chemistry The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters. Citation Rappoport, Dmitrij, Cooper J. Galvin, Dmitry Zubarev, and Alán Aspuru-Guzik. 2014. “Complex Chemical Reaction Networks from Heuristics-Aided Quantum Chemistry.” Journal of Chemical Theory and Computation 10 (3) (March 11): 897–907. Published Version doi:10.1021/ct401004r Accessed February 19, 2015 5:14:37 PM EST Citable Link http://nrs.harvard.edu/urn-3:HUL.InstRepos:12697373 Terms of Use This article was downloaded from Harvard University's DASH repository, and is made available under the terms and conditions applicable to Open Access Policy Articles, as set forth at http://nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of- use#OAP (Article begins on next page) Complex Chemical Reaction Networks from Heuristics-Aided Quantum Chemistry Dmitrij Rappoport,∗,† Cooper J Galvin,‡ Dmitry Yu. Zubarev,† and Alán Aspuru-Guzik∗,† Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA, and Pomona College, 333 North College Way, Claremont, CA 91711, USA E-mail: [email protected]; [email protected] Abstract While structures and reactivities of many small molecules can be computed efficiently and accurately using quantum chemical methods, heuristic approaches remain essential for mod- eling complex structures and large-scale chemical systems. Here we present heuristics-aided quantum chemical methodology applicable to complex chemical reaction networks such as those arising in metabolism and prebiotic chemistry. -
Introduction to Quantum Chemistry
Chem. 140B Dr. J.A. Mack Introduction to Quantum Chemistry Why as a chemist, do you need to learn this material? 140B Dr. Mack 1 Without Quantum Mechanics, how would you explain: • Periodic trends in properties of the elements • Structure of compounds e.g. Tetrahedral carbon in ethane, planar ethylene, etc. • Bond lengths/strengths • Discrete spectral lines (IR, NMR, Atomic Absorption, etc.) • Electron Microscopy & surface science Without Quantum Mechanics, chemistry would be a purely empirical science. (We would be no better than biologists…) 140B Dr. Mack 2 1 Classical Physics On the basis of experiments, in particular those performed by Galileo, Newton came up with his laws of motion: 1. A body moves with a constant velocity (possibly zero) unless it is acted upon by a force. 2. The “rate of change of motion”, i.e. the rate of change of momentum, is proportional to the impressed force and occurs in the direction of the applied force. 3. To every action there is an equal and opposite reaction. 4. The gravitational force of attraction between two bodies is proportional to the product of their masses and inversely proportional to the square of the distance between them. m m F = G × 1 2 r 2 140B Dr. Mack 3 The Failures of Classical Mechanics 1. Black Body Radiation: The Ultraviolet Catastrophe 2. The Photoelectric Effect: Einstein's belt buckle 3. The de Broglie relationship: Dude you have a wavelength! 4. The double-slit experiment: More wave/particle duality 5. Atomic Line Spectra: The 1st observation of quantum levels 140B Dr. Mack 4 2 Black Body Radiation Light Waves: Electromagnetic Radiation Light is composed of two perpendicular oscillating vectors waves: A magnetic field & an electric field As the light wave passes through a substance, the oscillating fields can stimulate the movement of electrons in a substance. -
Superconductivity and Unexpected Chemistry of Germanium Hydrides Under Pressure
Superconductivity and unexpected chemistry of germanium hydrides under pressure 1 1, 2, 3, 4, 1 1 M. Mahdi Davari Esfahani, Artem R. Oganov, ∗ Haiyang Niu, and Jin Zhang 1Department of Geosciences, Center for Materials by Design, and Institute for Advanced Computational Science, State University of New York, Stony Brook, NY 11794-2100, USA 2Skolkovo Institute of Science and Technology, Skolkovo Innovation Center, 3 Nobel St., Moscow 143026, Russia 3Department of Problems of Physics and Energetics, Moscow Institute of Physics and Technology, 9 Institutskiy Lane, Dolgoprudny City, Moscow Region 141700, Russia 4International Center for Materials Design, Northwestern Polytechnical University, Xi’an,710072, China (Dated: August 13, 2021) Following the idea that hydrogen-rich compounds might be high-Tc superconductors at high pressures, and the very recent breakthrough in predicting and synthesizing hydrogen sulfide with record-high Tc = 203 K, ab initio evolutionary algorithm for crystal structure prediction was employed to find stable germanium hydrides. In addition to the earlier structure of germane with space group Ama2, we propose a new C2/m structure, which is energetically more favorable at pressures above 278 GPa (with inclusion of zero point energy). Our calculations indicate metallicity of the new C2/m phase of germane with Tc = 67 K at 280 GPa. Germane is found to exhibit thermodynamic instability to decomposition to hydrogen and the new compound Ge3H11 at pressures above 300 GPa. Ge3H11 with space group I4¯m2 is found to become stable at above 285 GPa with Tc = 43 K. We find that the pressure-induced phase stability of germanium hydrides is distinct from its analogous isoelectronic systems, e.g., Si-hydrides and Sn-hydrides. -
Computational Analysis of the Mechanism of Chemical Reactions
Computational Analysis of the Mechanism of Chemical Reactions in Terms of Reaction Phases: Hidden Intermediates and Hidden Transition States ELFI KRAKA* AND DIETER CREMER Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, Texas 75275-0314 RECEIVED ON JANUARY 9, 2009 CON SPECTUS omputational approaches to understanding chemical reac- Ction mechanisms generally begin by establishing the rel- ative energies of the starting materials, transition state, and products, that is, the stationary points on the potential energy surface of the reaction complex. Examining the intervening spe- cies via the intrinsic reaction coordinate (IRC) offers further insight into the fate of the reactants by delineating, step-by- step, the energetics involved along the reaction path between the stationary states. For a detailed analysis of the mechanism and dynamics of a chemical reaction, the reaction path Hamiltonian (RPH) and the united reaction valley approach (URVA) are an effi- cient combination. The chemical conversion of the reaction complex is reflected by the changes in the reaction path direction t(s) and reaction path curvature k(s), both expressed as a function of the path length s. This information can be used to partition the reaction path, and by this the reaction mech- anism, of a chemical reaction into reaction phases describing chemically relevant changes of the reaction complex: (i) a contact phase characterized by van der Waals interactions, (ii) a preparation phase, in which the reactants prepare for the chemical processes, (iii) one or more transition state phases, in which the chemical processes of bond cleavage and bond formation take place, (iv) a product adjustment phase, and (v) a separation phase. -
Six Phases of Cosmic Chemistry
Six Phases of Cosmic Chemistry Lukasz Lamza The Pontifical University of John Paul II Department of Philosophy, Chair of Philosophy of Nature Kanonicza 9, Rm. 203 31-002 Kraków, Poland e-mail: [email protected] 1. Introduction The steady development of astrophysical and cosmological sciences has led to a growing appreciation of the continuity of cosmic history throughout which all known phenomena come to being. This also includes chemical phenomena and there are numerous theoretical attempts to rewrite chemistry as a “historical” science (Haken 1978; Earley 2004). It seems therefore vital to organize the immense volume of chemical data – from astrophysical nuclear chemistry to biochemistry of living cells – in a consistent and quantitative fashion, one that would help to appreciate the unfolding of chemical phenomena throughout cosmic time. Although numerous specialist reviews exist (e.g. Shaw 2006; Herbst 2001; Hazen et al. 2008) that illustrate the growing appreciation for cosmic chemical history, several issues still need to be solved. First of all, such works discuss only a given subset of cosmic chemistry (astrochemistry, chemistry of life etc.) using the usual tools and languages of these particular disciplines which does not facilitate drawing large-scale conclusions. Second, they discuss the history of chemical structures and not chemical processes – which implicitly leaves out half of the totality chemical phenomena as non-historical. While it may now seem obvious that certain chemical structures such as aromatic hydrocarbons or pyrazines have a certain cosmic “history”, it might cause more controversy to argue that chemical processes such as catalysis or polymerization also have their “histories”.