AFM, SPM
K. Mollet E. Leemans
I. L. Eremenko
A.A. Sidorov sidorov@igic.ras.ru
Formation of complex polynuclear complexes with the same or different metal atoms requires a different approach. If, in case of molecular structures in which the location of the metal centers, their electronic structure and packing in the crystal determines the physical properties of molecular materials (eg, magnetic, optical, catalytic), it is not always a simple self-assembly of such systems from simple components allow one to solve the problem of obtaining materials with desired characteristics. Here the correct choice of organic ligand- blocks often determines the outcome. Therefore, the organic component of the complex may be crucial in predicting how the synthetic methods and the final structure. It should also add that even the usual characteristics of a substance as its solubility in organic solvents, which is essential for certain future manufacturing operations, volatility, hydrolysis resistance and other can be given in the selection of the organic units in the assembly of polynuclear metal structures
The report examines examples of the use of various organic ligand-blocks in the chemical assembly of polynuclear metal architectures. Shows how to generate coordination magnetically active polymers, fluorescent clusters, polynuclear molecular precursors for various kinds of inorganic materials in the form of nanoscale films and crystals.
This study was supported by the Russian Foundation for Basic Research, the Council on Grants of the President of the Russian Federation, the State Department of Science and Innovation Policy, the Ministry of Education and Science of the Russian Federation, the Russian Academy of Sciences.
Short comment KO-13 ALEKSANDR MIKHAILOVICH BUTLEROV: AN
APPRECIATION
University of Southern California, Department of Chemistry, Los Angeles, California, USA
C.E. McKenna mckenna@usc.edu
With the enormous and ever accelerating acquisition of chemical knowledge over the past century and one decade into this one, that the work of a particular chemist carried out some 150 years ago could continue to impact modern research and teaching in organic chemistry is extraordinary. A perspective on A.M. Butlerov’s links and relevance to contemporary chemical science will be presented.
Section 1.
Theoretical Organic Chemistry:
Bonding, Structure and
Reactivity
1. Theoretical Organic Chemistry: Plenary lecture PL-1 TOPOLOGICAL PARADOXES OF THE
STRUCTURAL THEORY
Moscow State University, Chemistry Department, Moscow, Russia E.V. Babaev babaev@org.chem.msu.ru
The classical structural theory is still the “daily language” in synthetic chemistry. Its’
essence follows from the language of graph theory: for any set of K molecules, having in total V atoms and E bonds (obtained by arranging 2E valence electrons into E pairs, i.e.
into (2c,2e)-bonds) one can construct certain molecular graph with V vertices, E edges, and K components. This lead to simple balance eqn (1) for any molecule with localized bonds:
V – E = K – C (1).
Here C – is the “cyclicity” (number of independent cycles of size ≥3) in molecular graph. Shifting from graphs to 2D space-fill molecular models, the value C is equal to number of handles (“holes”) in the 2D surface of molecule. The eqn (1) can be easily expanded for multiple bonds (“2-mebered” cycles) and even to lone pairs (loops, a sort of
“1-membered” cycle) without loss of generality.
As was early shown by author [1-3], switch from graphs to hypergraphs (and from 2D surfaces to pseudo-manifolds) change eqn (1) to fundamentally new balance eqn (2):
2(V – E) = 2(K – C) + M – L (2).
Here M is index of multi-centered bonding, and L – the number of free radical centers. (E.g. L=1 for atom H, M=0 for molecule H2, M=1 for cation-radical H2+., M=2 for cations H3+, CH5+or allyl).
Importantly, the left part of eqn (2) correspond to particles (atoms V and electrons 2E), whereas right part of eqn (2) is their topology. Evidently, in any reaction the number of particles (ΔV and ΔE) is unchanged (material balance). Consequently, their overall topology is also unchanged, eqn (3):
2(ΔK – ΔC) + ΔM – ΔL = 0 (3).
Actually, eqn (3) is a new “Topology Conservation Law” for chemistry. Paradoxical consequence of eqn (3) is that our common chemical entities – cycles C, components K, free radical centers L and multi-centered bonds M – can not (dis)appear traceless, but only interchange to one another.
References:
[1]. Babaev E.V. Intuitive Chemical Topology Concepts. / In: Chemical Topology: Introduction and Fundamentals. Eds. Bonchev D., Rouvray R., 1999, Gordon & Breach Publ., Reading, pp.167-264.
[2]. Babaev E.V. The invariance of molecular topology in chemical reactions. / In: Graph theoretical approaches to chemical reactivity. Eds. Bonchev D., Mekenyan O. (Seria: Understanding Chemical Reactivity, Vol.9). Kluwer Academic Publ., Dordrecht-Boston-London, 1994, pp. 209-220.
[3]. http://www.chem.msu.ru/eng/misc/babaev/match/
1. Theoretical Organic Chemistry: Plenary lecture PL-2 THE "VALENCE STICK" IN ORGANIC MOLECULES:
FROM BUTLEROV TO MODERN UNDERSTANDING THE NATURE OF CHEMICAL BOND
Institute of Organoelement Compounds, Russian Academy of Sciences, Moscow, Russia
M.Yu. Antipin m_antipin@yahoo.com
Professor A. Butlerov was the first Russian chemist who understood in a full mere the meaning of the “valence stick” in organic compounds as an indication of some specific chemical interactions between atoms forming a molecule. From that time many other more and more sophisticated theories of the chemical structure were developed that explained successfully the spatial and electronic structure of myriads of molecules of interest in terms of chemical bonds (interactions) between atoms. Nowadays, modern very complicated quantum chemical molecular calculations and corresponding high accuracy experimental data are actively used in studies of chemical bonding. Amongst such calculations the Bader’s “Quantum Theory of Atoms in Molecules” (QTAIM) is often applied for many organic, organoelement and other compounds.
The QTAIM is based on analysis the topology of the full electron density distribution (EDD) function of the molecular system, and allows one to describe different characteristics of the chemical bonds in terms of observable (in contrast to the molecular orbital calculations) EDD characteristics. In particular, one of the most important topological features of the chemical bond is the so called “bond path” (bp) – the line (not necessary the straight one) of the maximum electron density in its 3-dimentional relief between two interacting atoms. The second criteria of a bond is presence of the “bond critical point”
(bcp) on the bp-line. The gradient of the EDD function vanishes in the bcp. If both the bp and bcp between two atoms exist – we have a chemical bond between them according to QTAIM. So, the “valence stick” in this theory attains more physically rigid meaning (as bp), and it might not be a straight line but may be curved like “bent bonds” in cyclopropanes, strained cage molecules and some other compounds.
It is also essential that EDD function and its topology may be reconstructed also from the high-resolution single crystal X-ray diffraction data that gives an attractive opportunity to compare directly the theory and experiment during chemical bond analysis. Results of similar analysis of chemical bonding will be demonstrated for a several series of organic and organoelement compounds for which non-typical chemical bonds were observed.
1. Theoretical Organic Chemistry: Plenary lecture PL-3 EXTRAORDINARILY LONG 2.9 Å AND
MULTICENTER C-C BONDS - WHAT IS A CHEMICAL BOND?
University of Utah, Department of Chemistry, Salt Lake City, USA J.S. Miller jsmiller@chem.utah.edu
Carbon-carbon (CC) bonding is a key essence of organic and biochemistry. The length of a CC bond, i.e. 1.54 Å found in the diamond allotrope of carbon, is among the essential information learned by all organic chemistry students. This is the length of a single bond (σ) between sp3-hybridized carbons and is the longest of all common CC bonds.
Our studies of the [TCNE]22- (TCNE = tetracyanoethylene) dimers reveal that 2.90 ± 0.05 Å 2 electron/4 center (2e-/4c) CC bonds are present. Structural, spectrsocopic, magnetic and computational data supporting this multicenter formulation will be presented. These unusual bonds lead to unusual physical properties that will be discussed, as will what is a bond?
Futhermore, examples of long, multicenter C-C bonds existing for other dianions, e.g., [cyanil]22-, as well as dications, e.g., [TTF]22+ (TTF= tetrathiafulvalene), and homo-, e.g., [tri-t-butylphenalenyl]2, and hetrodimers e.g., [TTF•••´TCNE], will be described.
1. Theoretical Organic Chemistry: Plenary lecture PL-4 UNEXPECTED CLEAVAGE OF ACETYLENIC MOIETY IN ALPHA-KETOACETYLENES UNDER
INFLUENCE OF 1,2-DIAMINOETHANE: NEW ROUTE TO 2-SUBSTITUTED IMIDAZOLINES 1 - Institute of Chemical Kinetics and Combustion of the Russian Academy of Sciences, Novosibirsk, Russia
2 - Novosibirsk Institute of Organic Chemistry of the Russian Academy of Sciences, Novosibirsk, Russia
S.F. Vasilevskiy1 M.P. Davydova1
G.A. Tolstikov2 vasilev@kinetics.nsc.ru
Although acetylenes are well-recognized as convenient building blocks for many useful transformations for organic synthesis, medicinal chemistry, and materials science, their synthetic potential is far from full utilization of unique reactivity of triple bonds.
For preparing of heterocyclic compounds we used perspective synthetic methodology - reactions of polyfunctional reagents (NH2CH2CH2NH2, NH2NH2, NH2OH, NH2-C(=NH)- NH2 etc.) with α-ketoacetylenes [1,2]. Such methology allow us to prepare some pyrazole, isoxazole, pyrimidine derivatives (these modifications will be presented). But more remarkable transformation we found analyzing of reaction of activated acetylenes with 1,2- diaminoethane
Ar
Ar'
O
NH2CH2CH2NH2 Ar Ar'
O HN
NH2
Ar O
N Ar' NH dioxane
reflux
This work presents example of cleavage of C≡C moiety in α-ketoacetylenes by interaction with 1,2-diaminoethane in boiling dioxane with the formation of corresponding methylaryl ketones (40-50%) and 2R-substituted 4,5-dihydro-1H-imidazoles (40-45%).
We observed and isolated intermediates of above mention reaction – product of addition of 1,2-diaminoethane to triple bond - 3-(2-aminoethylamino)-3-(Ar)-1-(Ar’)-prop- 2-en-1-ones (10-15%).
This reaction can be considered as a cleavage of C≡C moiety via disproportionation.
Mechanism of these transformations will be discussed.
References:
1. Vasilevsky, S. F., Davydova, M. P., Tolstikov, G. A., Chem. Heterocycl. Compd., 2008, 44, 1257-1261 (Engl.Transl.)
2. Davydova, M. P., Vasilevsky, S. F., Tolstikov, G. A., Russ. Chem. Bull., Int. Ed., 2011, 1, 1-2
This work was supported by the Interdisciplinary Grant No.93 of SB of the Russian Academy of Sciences (2009–2011), Grant RFBR No.10-03-00257-a (2010–2012), Grant 5.9.3. of the Russian Academy of Sciences (2009–2011) and the Chemical Service Centre of SB RAS.
1. Theoretical Organic Chemistry: Oral report O-1 QUANTITATIVE STRUCTURE-PROPERTY RELATIONSHIPS: RECENT APPROACHES Moscow State University, Department of Chemistry, Moscow, Russia V.A. Palyulin
N.S. Zefirov vap@org.chem.msu.su
QSAR/QSPR (quantitative structure-activity/property relationships) approaches can be considered as universal techniques for modeling and prediction of numerous properties of chemical compounds and materials. These approaches are based on the correlations of property values with the parameters (descriptors) of chemical structures. The structure- property relationships are evaluated using various statistical methods, artificial neural networks, etc. The developed structure-property model can be used for the prediction of properties of new chemical compounds for which these properties were never studied or even the compounds themselves were never synthesized. A large number of physico- chemical properties were modeled for various organic compounds basing on their structural formulas. Some properties of materials can be predicted as dependent on the structure of small molecules used as additives (e.g. antioxidants). Good results were obtained for the prediction of diffusion coefficients of small molecules in polymers.
Prediction of biological activity for organic compounds is one of the most challenging problems. For that purpose we proposed Molecular Field Topology Analysis (MFTA) which involves the construction of a molecular supergraph (a simple graph such that the molecular graphs of all training set structures can be represented as its subgraphs).
A uniform descriptor set is obtained by superimposing each training set structure onto the molecular supergraph. For each supergraph vertex the values of atomic charge, van der Waals radius and other local parameters for the respective atom in a particular structure are assigned. For unoccupied vertices the neutral descriptor values are used. The analysis of the impact of local descriptors on the activity for supergraph positions is highly helpful in the design of new active structures. The developed structural generators in conjunction with MFTA significantly increase the efficiency of the design of active structures.
1. Theoretical Organic Chemistry: Oral report O-2 FROM COMPUTATIONAL PHOTOBIOLOGY TO THE
DEVELOPMENT OF BIOMIMETIC MOLECULAR DEVICES
University of Siena, Department of Chemistry, Siena, Italy M. Olivucci olivucci@unisi.it
During the last few years we have started to explore the possibility of designing and synthesizing molecules that could mimic the photoisomerization of the visual pigment Rhodopsin and, in particular its low-temperature photochromism [1]. When embedded in the opsin cavity the Rhodopsin chromophore (i.e. the protonated Schiff base of retinal) displays an ultrafast and stereoselective photoisomerization with high quantum yield. In order to design a chromophore displaying a similar efficiency in common solvents we have been looking at diverse alkylated Schiff bases featuring a single isomerizable double bond.
In this lecture we show that the indanylidene-pyrroline (NAIP) framework [2-4] provides a computationally and synthetically viable prototype for the development of systems that reproduce the excited state electronic structure and photoisomerization dynamics of Rhodopsin in methanol or water. We will also show that, on the basis of these studies we have been able to achieve systems that, in perspective, can be used as electrostatic switches. In fact, we have been able 5to design an unprecedented “dipole” switch capable of inverting, reversibly, its ca. 15 D dipole moment upon double bond photoisomerization [5].
References:
[1] Shapiro I., Ryazantsev M. N., Frutos L.-M., Ferré N., Lindh R. & Olivucci M. (2011) J Am Chem Soc 133:3354-3364.
[2] Lumento F., Zanirato, V., Fusi, S., Busi, E., Latterini, L., Elisei, F., Sinicropi, A., Andruniów, T., Ferré, N., Basosi, R. & Olivucci, M. (2007) Angew Chem Int Ed Engl 46:414-420.
[3] Sinicropi A., Martin, E., Ryasantsev, M., Helbing, J., Briand, J., Sharma, D., Léonard, J., Haacke, S., Cannizzo, A., Chergui, M., Zanirato, V., Fusi, S., Santoro, F., Basosi, R., Ferré, N. & Olivucci, M. (2008) Proc. Nat. Acad. Sci. USA 105:17642-17647.
[4] Briand J., Bräm, O., Réhault, J., Léonard, J., Cannizzo, A., Chergui, M., Zanirato, V., Olivucci, M., Helbing, J. & Haacke, S. (2010) Phys Chem Chem Phys 12:3178 - 3187.
[5] Melloni A., Rossi Paccani, R., Donati, D., Zanirato, V., Sinicropi, A., Parisi, M. L., Martin, E., Ryazantsev, M., Ding, W. J., Frutos, L. M., Basosi, R., Fusi, S., Latterini, L., Ferré, N. & Olivucci, M.
(2010) J Am Chem Soc 132:9310-9319.
1. Theoretical Organic Chemistry: Oral report O-3 SULFLOWER AND OTHER CHEMICAL FLOWERS Moscow State University, Department of Chemistry, Moscow, Russia V.G. Nenajdenko nen@acylium.chem.msu.ru
Recently we have described synthesis of the first fully heterocyclic circulene Sulflower 1, which is a new type of heterocyclic molecules. The properties of Sulflowe were comprehensively studied, including fabrication of field-effect transistors. Reaction of initial tetrathiophene 2 with selenium under standard and variously modified conditions leads to formation of target sulfur- selenium circulene 3 and "dehydrohelicene" 4. The synthesis of others heterocyclic circulenes is now in progress.
S S
S S
S S
S S
S
S
S
S
S S
S S
Se
Se
Se S S
S S
Se
Se
Se
Se a) 16 eq. LDA + 16 eq. sulfur, Et2O
b) 16 eq. LDA + 16 eq. selenium, Et2O c) HCl
d) vacuum sublimation
1 2 3 4
+
a, c, d b, c, d
S S
S S
RN
S
NR
S
N N
N N
N N
X X
X X
X X X X
X X X X
X= CH, N
N N
N
N N
N N N
N
1. Theoretical Organic Chemistry: Oral report O-4 INTERIONIC INTERACTIONS AND THEIR IMPACT ON STRUCTURE AND PROPERTIES OF SOME IMIDAZOLIUM- AND PHOSPHONIUM-BASED IONIC
LIQUIDS
1 - A.E. Arbuzov Institute of Organic and Physical Chemistry, Kazan Scientific Centre of the Russian Academy of Sciences, Department of Physical Chemistry, Kazan, Russia
2 - Ecole Polytechnique Federale de Lausanne (EPFL), Institut des Sciences et Ingenierie Chimiques, Lausanne, Switzerland
S.A. Katsyuba1 E.E. Zvereva1 T.P. Gryaznova1
P.J. Dyson2 V.V. Ermolaev1 V.A. Miluykov1
O.G. Sinyashin1 katsyuba@iopc.ru
Density functional theory combined with X-ray crystallography, IR and NMR spectroscopy has been used to study interionic interactions and structure of several imidazolium- and phosphonium-based ionic liquids (ILs).
Multiple short contacts between the counterions are typical for the both kinds of ILs in crystals, melts and solutions. Various modes of ion pairing and their spectral manifestations have been found; the CH-groups of the imidazolium ring form hydrogen bonds with the halides and such weakly-coordinating anions as BF4-, PF6-, Tf2N-, while only halides are able to pronounced H-bonding with the CH-groups of tetraalkylphosphonium cations. This fundamental difference between the halides and the perfluoro anions causes essential differences in structure of the corresponding ILs. Namely, ILs based on the weakly-coordinating anions can be regarded as consisting of the ion pairs, while both the imidazolium and the phosphonium halides represent a network of the counterions bonded by strongly anti-cooperative hydrogen bonds.
It is demonstrated that neither the energy of ion pairing nor specific capability to hydrogen bond formation of various ILs explain the differences in their melting points.
However the analysis of potential energy surfaces of ion pairs within the framework of a simple anharmonic oscillator model allows rationalization and prediction of melting points (Tm.p.) and heat capacities (Cp) of ILs. Possible influence of the cation conformation on Cp
and Tm.p. of the ILs. is discussed in the context of this theoretical model.
Financial support of Switzerland-Russia S&T Cooperation Program is gratefully acknowledged
1. Theoretical Organic Chemistry: Oral report O-5 CHEMILUMINESCENCE FROM ORGANIC REACTIONS. FUNDAMENTALS AND APPLIED
ASPECTS
Institute of Organic Chemistry, Ufa Scientific Center of the RAS, Ufa, Russia
D.V. Kazakov dkazakov@anrb.ru
The process of transforming chemical energy into light emission has been an attractive topic of intensive research over the years, in view of its fundamental mechanistic significance and the diversity of practical applications. Bio- and chemiluminescence (CL), the emission of light in biochemical and chemical reaction, is wildly used in technology, biology and medicine. On the other hand, the in-depth knowledge of CL systems paves the way for understanding the otherwise difficult to explore “dark” processes associated with such reactions.
In this report, important role of CL in organic chemistry is discussed. Brightly emitting organic peroxides-based biological systems are illustrated. Relation between fundamental significance of CL phenomenon and its practical applications in medicine and biochemistry is demonstrated by the reactions of cyclic peroxides 1,2-dioxetanes, a kind of energy storage system. Special attention is given to our recent results obtained in the field of chemistry and chemiluminescence of high-energy organic peroxides:
- A new type of chemiexcitation for liquid-phase organic reactions is reported (oxygen- transfer chemiluminescence) which is realized during oxidation of saturated hydrocarbons by dioxiranes.1 A novel mechanisms of light generation in the reactions of peroxides with luminescent lanthanide complexes are described.
- A key role of singlet oxygen, oxidant and important intermediate of chemical and biochemical processes, in freshly discovered light emitting peroxide reactions is demonstrated.2,3
- A new promising direction of research is introduced: chemistry and chemiluminescence of pharmacologically valuable organic peroxides − 1,2,4,5-tetroxanes and 1,2,4-trioxolanes.
Achievements and applied perspectives of the area are discussed.4
References:
1. Kazakov D.V., Barzilova A.B., Kazakov V.P., Chem. Commun., 2001, 191.
2. Adam W., Kazakov D.V., Kazakov V.P., Chem. Rev., 2005, 105, 3371.
3. Kazakov D.V., Kazakov V.P., Maistrenko G.Ya., Mal’zev D.V., Schmidt R., J. Phys. Chem. A, 2007, 111, 4267.
4. Kazakov D.V., Kazakova O. B., Ishmuratov G.Yu., Terent’ev A.O., Nikishin G.I., Tolstikov G.A. Dokl.
Ak. Nauk, 2011, 436, 774.
This work was supported by RFFI, project 09-03-00831a.
1. Theoretical Organic Chemistry: Oral report O-6 REACTIVITY OF THIOPHENOLATE TOWARD
CHALCOGENADIAZOLES 1 - Institute of Chemical Kinetics and Combustion 2 - Novosibirsk Institute of Organic Chemistry N.P. Gritsan1