Homolytic addition of dithiols to alkynes: A new approach to the construction of dithiacyclanes and crown thioethers

A novel general approach to the construction of sulfur-containing heterocyclic compounds and crown thioethers based on one-pot “assembling” of their molecules from α,ω-dithiols and alkynesvia homolytic cycloaddition has been developed. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 7, pp. 1256–1267, July, 1997.     

Evaluating molecular asymmetry

A method for calculating the asymmetry parameters of molecules based on Avnir’s CSM approach combined with the “dissymmetry function” method is suggested. The performance of the approach is demonstrated on various geometrical models — high-symmetry antiprisms of S₁₀ and D₅ symmetry groups, helices, and molecular objects. It is shown that the MCSM method unambiguously determines the symmetry element or estimates the degree of asymmetry for molecules from different structural classes. A. V. Bogatskii Physiocochemical Institute, Ukrainian Academy of Sciences. Odessa State University. Translated fromZhurnal Strukturnoi Khimii, Vol. 39, No. 3, pp. 547–552, May–June, 1998.     

Computational Study of Supramolecular Bis-porphyrin “Molecular Tweezers”

A computational study of a series of space separated bis-porphyrin “molecular tweezers” using semiempirical (AM1) and DFT (B3LYP and PBE1PBE) methods has been carried out. It was found that polynorbornane bis-porphyrin systems are significantly less rigid than previously thought. The variation of the metal–metal separation distance between the two porphyrin centers does not cause a significant energy change thus enabling these molecules to easily adjust to the optimal coordination distance required for complexation by various bidentate 4-pyridyl ligands inside the cavity of these “tweezers”. Article 54, ECCC-10, April 1-30 2005, http://www.eccc.monmouth.edu     

Quantum-Chemical Study of “Hydride” Mobility in the Molecules of Chalcogenopyrans

An approach is proposed for the quantum-chemical investigation of “hydride ion” transfer based on analysis of the similarity of the order of variation in the ionization potentials, enthalpies, and free energies of affinity to the hydride ion, the hydrogen atom, and the proton in the substrate molecules and also the derivatives of their cations, radicals, and ions to the experimentally established “hydride” series. It was established that the experimental “hydride” mobility series of six chalcogenopyrans based on “semicyclic” 1,5-diketones agrees with the quantum-chemically calculated ionization potentials of the molecules and with the affinity of the respective radicals to the hydrogen atom participating in the transfer. It was found that direct removal of a hydride ion and initial deprotonation of the substrates followed by the removal of two electrons are unlikely. “Hydride” shift mechanisms, in which the first stage is transfer of an electron or hydrogen atom from the chalcogenopyran molecules, are feasible. __________ Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 9, pp. 1305–1311, September, 2005.     

On the origin of Baeyer strain in molecules – an ab initio and DFT analysis

It is shown that destabilization energy of organic molecules containing small rings can be estimated by quasi–homodesmotic reactions involving acyclic “strain–free” counterparts. These destabilization energies E_s can be well reproduced at the HF level employing cc-pVTZ basis set, because the contributions of the electron correlation and ZPV energy practically cancel each other in most cases. A predominating factor leading to a decreased stability of molecules involving small ring fragments is given by the Ω bond bending or Baeyer strain. It leads to a dramatic decrease in the electron–nuclei attraction, which is a hallmark of the angular strain. Similar results are obtained by the DFT–B3LYP method. It is strongly pointed out that Baeyer strain cannot be singled out from the total destabilization energy in a precise quantitative way, since it is interlocked with other types of intramolecular interactions like the nonbonded repulsions, a significant increase in the stability of the CH bonds emanating from the small cyclic structures and by the σ–aromaticity or σ–antiaromaticity in three– and four–membered rings, respectively. Nevertheless, it is fair to say that Baeyer strain is the essential factor in determining decreased stability of small ring compounds and that the diminished electron–nuclear attraction is its characteristic signature at the global level. Dedicated to Professor Karl Jug on the occasion of his 65th birthday.     

Host-molecule-coated quantum dots as fluorescent sensors

“Host” molecules, containing a binding site that is highly specific for an analyte “guest,” are used as sensors to register analyte binding through a variety of mechanisms such as colorimetric, fluorescent, or electrochemical signals. There is increasing interest in the host–guest chemistry on the surface of quantum dots (QDs) and in the changes that it produces in the luminescent properties of QDs. The bulk of this study focuses on those QDs with bound host molecules (crown ether, cyclodextrin, calixarene, and porphyrin) and the selectivity they display toward metal ions and small organic molecules.     

Standardization of pH measurements based on the ion interaction approach

The Pitzer method was used to calculate the pH values on the conventional and “true” scales for the TRIS—TRIS·HCl−NaCl−H₂O buffer system in the 0–40 °C temperature region and 0–4 NaCl molality interval. This buffer can be used as a standard for pH measurements in a wide range of ionic strengths. The conventional scale is used in cells without a salt bridge. The “true” scale is recommended for pH measurements using cells with a salt bridge. At the same concentrations of the buffer solution, the “true” scale is essentially transformed into the scale of the National Bureau of Standards (NBS) of the USA. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 4, pp. 676–680, April, 2000.     

Structural transition to electrolyte-water solvent and changes in the molecular dynamics of water and properties of solutions

A model of concentration transition “ions and complexes in a water structure → ionic and ionicaqueous clusters → polymer structures of salt and crystal hydrate melts” is suggested. The appearance of cluster nanostructures outside the first zone of a waterlike structure is regarded as a general characteristic of solutions. The characteristics of solutions, phase equilibria, and salts of complex composition are interpreted based on this model. Investigation of the complex dielectric constant of electrolytic solutions in the SHF and EHF bands (7–119 GHz) at high concentrations showed that there are two dispersion regions in which the relaxation times differ by a factor of 5–10. Relaxation processes are separated, the numbers of molecules in hydration shells are calculated, and relaxation times are determined for bulky tetrahedral water with hydration shells of ions, for clusters, and for ionicaqueous polymer chains. It is shown that the two structure subsystems of water molecules in concentrated solutions may be described using the limited rotator/generalized diffusion molecular model. Translated fromZhumal Strukturnoi Khimii, Vol. 39, No. 5, pp. 851–863, September–October, 1998.     

Origin of “cold” water molecules in the composition of low-molecular-mass products of the mechanical fracture of poly(methyl methacrylate)

A hypothesis on the correlation between the origin of “cold” (∼53 K) water molecules released by a growing crack and a low (∼123 K) temperature of stretched and then thermoelastically cooled polymer chains that ruptured at the crack top is advanced. A mechanism behind the formation of “cold” water molecules is suggested. It includes their “soft” desorption due to mechanical action onto thermoelastically cooled side groups with adsorbed cooled water molecules from an unloading wave that is induced by the rupture of the main chain and that travels along it.     

Phase equilibria in binary subsystems of urea–biuret–water system

Joint results of the differential scanning calorimetry (DSC) and thermogravimetry (TG) experiments were the basis for the fusion enthalpy and temperature determination of the biuret (NH₂CO)₂NH (synthesis by-product of the urea fertilizer (NH₂)₂CO). Recommended values are Δ_m H = (26.1 ± 0.5) kJ mol⁻¹, T _m = (473.8 ± 0.4) K. The DSC method allowed for the phase diagrams of “water–biuret,” “water–urea,” “urea–biuret” binary systems to be studied; as a result, liquidus and solidus curves were precisely defined. Stoichiometry and decomposition temperature of the biuret hydrate identified, composition of the compound in “urea–biuret” system was suggested.     

Structures of deoxypeganine salts

The structures of deoxypeganine (DOP) hydrochloride and oxalate were solved by x-ray structure analysis. An infinite chain along the crystallographic c axis was formed in the crystal structure of DOP oxalate. A molecular framework consisting of Cl anions and DOP cation protonated at N1 was found in the structure of unhydrated DOP hydrochloride. The molecular packing of the “host” (DOP cation) was pseudoisostructural in the studied ion-molecular crystals but differed from other known DOP salts. The “guest” molecules (acid anions) in the studied and known DOP salts formed different intermolecular contacts. __________ Translated from Khimiya Prirodnykh Soedinenii, No. 3, pp. 280–283, May–June, 2006.     

The transition of spontaneous polymerization of acrylamide to “explosive” regime

Experimental results related to the transition of spontaneous polymerization of acrylamide complexes with metal nitrates to the “explosive” regime at room temperature are presented. It is suggested that the “explosion” has a thermal nature. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 4, pp. 859–861, April, 1997.     

Cooperative effects in polymolecular nitrogen clusters

The structures and stabilities of the van der Waals clusters (N₂) _n (n = 2–8) have been evaluated using ab initio calculations at the MP2(full)/6–311+G* and CCSD(full)/6–311+G* level of theory. At n = 2–4, the formation of planar and three-dimensional structures is possible. At n > 4, only “globular” structures can be formed, whose formation energies increase with the cluster size. As the number of interacting molecules increases, the examined systems exhibit cooperative effects associated with non-additive enhancement of nonbonded intermolecular interactions.     

Development of small molecules designed to modulate protein–protein interactions

Summary Protein–protein interactions are ubiquitous, essential to almost all known biological processes, and offer attractive opportunities for therapeutic intervention. Developing small molecules that modulate protein–protein interactions is challenging, owing to the large size of protein-complex interface, the lack of well-defined binding pockets, etc. We describe a general approach based on the “privileged-structure hypothesis” [Che, Ph.D. Thesis, Washington University, 2003] – that any organic templates capable of mimicking surfaces of protein-recognition motifs are potential privileged scaffolds as protein-complex antagonists – to address the challenges inherent in the discovery of small-molecule inhibitors of protein–protein interactions.This paper is adapted from a presentation at the 230th National Meeting of the American Chemical Society, Washington DC, August 28 – September 1, 2005, Abstract COMP-136.     

Nature of paramagnetic centers in polyaniline as studied by SQUID magnetometry

The temperature and field dependences of the magnetic moment of polyaniline powder doped by m-cresol were measured by SQUID magnetometry in the temperature range 2–300 K at 1000 Oe and in the range 0–50000 Oe at 2 K, respectively. The field dependence is not described by the Brillouin function for spin 1/2, as is expected in the framework of a commonly accepted “metallic” model. Both dependences are quite correctly described by a “triplet” model using a distribution of singlet-triplet splitting (E) with the density distribution function having a narrow peak near E = 0.     

Distances and volumina for graphs

It has long been realized that connected graphs have some sort of geometric structure, in that there is a natural distance function (or metric), namely, the shortest-path distance function. In fact, there are several other natural yet intrinsic distance functions, including: the resistance distance, correspondent “square-rooted” distance functions, and a so‐called “quasi‐Euclidean” distance function. Some of these distance functions are introduced here, and some are noted not only to satisfy the usual triangle inequality but also other relations such as the “tetrahedron inequality”. Granted some (intrinsic) distance function, there are different consequent graph-invariants. Here attention is directed to a sequence of graph invariants which may be interpreted as: the sum of a power of the distances between pairs of vertices of G, the sum of a power of the “areas” between triples of vertices of G, the sum of a power of the “volumes” between quartets of vertices of G, etc. The Cayley–Menger formula for n-volumes in Euclidean space is taken as the defining relation for so-called “n-volumina” in terms of graph distances, and several theorems are here established for the volumina-sum invariants (when the mentioned power is 2). This revised version was published online in July 2006 with corrections to the Cover Date.     

Force fields of halide-substituted methane derivatives

The paper describes methods for determining the force fields of large sets of molecules which share the common property that in their constituent groups of molecules the equivalent force constants always change monotonically with the properties of substituent atoms belonging to the same subgroup of the periodic table. The force fields of the CH_4−nX_n (n=0–4, X=F, Cl, Br, I) molecules of the methane series are obtained. The applications of these force fields are discussed. In particular, they can serve as a basis for a data bank of the force fields of fragments suitable for constructing the force fields of more complex molecules. Russian Scientific Center “Applied Chemistry”, St. Petersburg. Translated fromZhurnal Strukturnoi Khimii, Vol. 37, No. 2, pp. 250–256, March–April, 1996. Translated by I. Izvekova     

Effect of ligand coordination type on the relative stability of linear mercury clusters

The problem of stabilization of linear mercury clusters with acceptor ligands coordinated along the symmetry axis of the cluster is discussed in terms of the MNDO method. It is shown that stable four-membered rings Hg₂Cl₂ may be formed. It is proposed that the structure of linear mercury clusters with side coordination of ligands be described as the result of “polymerization” of short stable linear molecules XHg_nX (n=1, 2) and HgX ₂ ¹⁻ , HgX ₃ ¹⁻ ions with accepting terminal groups. Mordovia State University. Institute of Organoelement Compounds, Russian Academy of Sciences. Translated fromZhurnal Strukturnoi Khimii, Vol. 39, No. 1, pp. 26–34, January–February, 1998. This work was performed in the framework if the interindustry scientific and technical program “Fullerenes and Atomic Clusters.”     

Synthesis of racemic 10-methyltridecan-2-one,the sex pheromone ofDiabrotica undecimpunctata

A new synthesis of racemic 10-methyltridecan-2-one, the sex pheromone ofDiabrotica undecimpunctata Howardi has been effected. “InterBAV” Scientific Production Company RM, Kishinev. Translated from Khimiya Prirodnykh Soedinenii, No. 4, pp. 558–560, July–August, 1994.     

Aromaticity in heterocycles: new HOMA index parametrization

Abstract  

A new parametrization for the Harmonic Oscillator Model of Aromaticity (HOMA) index to determine aromaticity of heterocycles is introduced. The new HOMA for Heterocycle Electron Delocalization (HOMHED) is based on the experimental data from electron diffraction X-ray for the reference molecules used to estimate the simple, double, and optimal bond lengths. Bond length of “pure” single and double bonds of non-conjugated systems or systems without π-electrons and/or n-electron delocalization were considered. The HOMHED index was determined for a series of five and six heterocycles with C–C, C–N, C–O, C–S, N–N, N–O, and N–S bonds. The π-electron delocalization of these heterocycles was determined by Krygowski-reformulated HOMA and HOMHED and it was proved that HOMHED worked in line with HOMA for all heterocycles, except those containing oxygen, which were found to be weak aromatic from Krygowski rHOMA calculations.