Mutual Orientation Of Molecules Research Articles

X-ray diffraction and theoretical study of molecular and crystal structure of new crystalline aryl- and alkyl-substituted N-(adamantan-1-yl)amides: Similarities and differences

The molecular structure and crystal packing of new aryl and alkyl N-(adamantan-1-yl)amides derivatives А1–А7 were analyzed, and their intermolecular interaction parameters were found using X-ray diffraction, topological analysis within Bader's theory of “Atoms in molecules”, PIXEL method, and Hirshfeld surface analysis. N–H…O and С–Н…О hydrogen bonds and numerous Н…Н contacts are formed in the crystals of adamantylamides А1–А7. The adamantylamide molecules A1–A7 form a С(4) supramolecular chain synthon via N–H…O hydrogen bonds. An acetamide oxygen atom in the crystals of A1, A3–A5, and A7 is involved into unsymmetrical bifurcated bonds, in which one component is N–H…O and the other one is С–Н…О. The contribution of the O…Н contacts to the Hirshfeld surface is higher for alkyl adamantylamides than that for the aryl derivatives, whereas the packing index is lower for the alkyl derivatives than that for aryl one. The position of an acetamide group relative to adamantane framework in all structures is fixed by C–H…O intramolecular hydrogen bonds. The stabilization energy of the molecular pairs apparently depends on orientation of substituents and the mutual orientation of molecules in the pair that create favorable conditions for numerous intermolecular interactions.

Multiscale modeling of active layer of hybrid organic-inorganic solar cells for photovoltaic applications by means of density functional theory and integral equation theory of molecular liquids

Photovoltaic devices convert solar energy into electricity and are promising candidates to reduce carbon emission while providing an alternative way to meet increasing demand in energy consumption. In recent years, organic or hybrid organic-inorganic photovoltaic devices demonstrate steady increase in performance and stability and a promising tendency toward the low production cost. To make them attractive for commercial production, however, a deep understanding and ability to predict physical, chemical and electrochemical processes occurring in photovoltaic conversion layer is needed. Here, we present multiscale modeling of electronic and structural properties of hybrid organic-inorganic perovskites (OIP) of the type CH3NH3PbX3, X = Br, Cl, I, in contact with organic molecules of P3BT, P3HT, or SQ02, including adsorption on inorganic substrates of TiO2. Our methodology is based on Density Functional Theory (DFT) and integral equation theory of molecular liquids in the Reference Interaction Site Model (RISM). We apply it to study the photovoltaic thin film nanomorphology and determine the key factors affecting the performance of OIP-based bulk heterojunction solar cells through their influence on charge separation, charge transport and recombination losses in donor-acceptor blends. These factors include chemical composition of heterojunctions and mutual orientation of molecules on the border of the donor-acceptor or donor-acceptor-substrate systems. Since the formation of thin active layer of solar cells occurs in fluidic phase, we also provide a detailed microscopic insight into the organization of solvent molecules in the solvation shell structure and their contribution to the solvation thermodynamics. In total, these properties define charge transfer processes from donor to acceptor and are utilized in development of new generation organic and hybrid organic-inorganic solar cells. The calculated nanoscale morphologies serve as a guide in rational design of organic or hybrid photovoltaics.

X-ray study of the molecular structure and of the internal ordering degree in 1,3,5–tri-tert-butylbenzene at 363 K

The paper presents the structure and molecular correlations in liquid 1,3,5–tri-tert-butylbenzene C6H3[C(CH3)3]3 determined for the first time by the X-ray diffraction method. Experimental function i (S) was determined by X-ray scattering from a liquid sample and compared with the theoretical function im(S) calculated for the most probable assumed model of the 1,3,5–tri-tert-butylbenzene structure. The most probable parameters of molecule 1,3,5–tri-tert-butylbenzene were determined from the detailed analysis of the differential radial distribution function of electron density. Theoretically calculated parameters were compared with experimentally measured data. Good agreement between the theoretical and experimental curves is obtained on assuming the statistically most probable model of this molecule. The mean bond length between a C atom in an aromatic ring and the central C atom of a tert-butyl group, the bond C(1)−C(7) is 1.54 Å. Local, most probable manners of packing and mutual orientation of molecules within the space of the first coordination sphere are discussed. The local structure of the liquid 1,3,5–tri-tert-butylbenzene is similar to the crystalline structure of the compound.

Sub-nanometer resolution of an organic semiconductor crystal surface using friction force microscopy in water

Organic semiconductors (OSC) are attracting much interest for (opto)electronic applications, such as photovoltaics, LEDs, sensors or solid state lasers. In particular, crystals formed by small -conjugated molecules have shown to be suitable for constructing OSC devices. However, the (opto)electronic properties are complex since they depend strongly on both the mutual orientation of molecules as well as the perfection of bulk crystal surfaces. Hence, there is an urgent need to control nano-topographic OSC features in real space. Here we show that friction force microscopy in water is a very suitable technique to image the free surface morphology of an OSC single crystal (TDDCS) with sub-nanometer resolution. We demonstrate the power of the method by direct correlation to the structural information extracted from combined single crystal (SC-) and specular (s-) XRD studies, which allows us to identify the pinning centers encountered in the stick-slip motion of the probing tip with the topmost methyl groups on the TDDCS surface.

Raman study of solvation in solutions of lithium salts in dimethyl sulfoxide, propylene carbonate and dimethyl carbonate

Raman study of cation and anion solvation in dimethyl sulfoxide, propylene carbonate and dimethyl carbonate solutions of six lithium salts has been performed in the concentration range from 0.05 to 0.25 molar fraction of a salt. The dependences of the amount of the solvent particles involved in dimerization, hydrogen bonding, and solvation have been determined, and the mean solvation numbers have been found. It is concluded that in all solutions studied, notwithstanding the differences in the physical properties of the solvent and in the structure of the anion, both the lithium cation and the anion solvation equilibria are quantitatively similar. In all cases, solvation numbers of cations are close to two and do not vary with the growth of concentration. In particular, in molten LiX·4S solvates, LiS4+ entities expected from the phase diagrams do not exist. It has been found that for the solvent molecules in dimers and in solvation spheres, non-coincidences between vibrational frequencies of isotropic and anisotropic lines, ΔνNCE=νaniso−νiso are of opposite signs signifying that the mutual orientation of molecules is different. In all systems studied, solvation numbers of anions decrease if the salt content is growing and are close to four in concentrated solutions. These striking similarities in the structure and concentration of solvated entities clearly signify that solvation phenomena have no decisive importance in determining the properties of salt systems.

Cocrystals of fisetin, luteolin and genistein with pyridinecarboxamide coformers: crystal structures, analysis of intermolecular interactions, spectral and thermal characterization

Fisetin, luteolin and genistein, natural polyphenolic compounds of pharmaceutical interest, were combined with nicotinamide and isonicotinamide with an aim to obtain their cocrystals. A screening experiment utilizing solvent-drop grinding was conducted for those combinations. Cocrystalline phases were identified by XRPD and, as far as possible, obtained as single crystals in solution evaporation approach. Five new cocrystals were isolated, characterized by X-ray single-crystal diffraction, FT-Raman spectroscopy, thermal analysis (DSC and TG–DTA), 1H NMR in solution and compared in terms of supramolecular motifs. Reported herein fisetin–nicotinamide (1 : 2) ethanol hemisolvate (FisNam), fisetin–isonicotinamide (1 : 1) (FisInam), two polymorphic forms of luteolin–isonicotinamide (1 : 1) (LutInam, LutInam2) and genistein–nicotinamide (1 : 1) monohydrate (GenNam) cocrystals reveal the presence of an O–H⋯Narom heterosynthon between an O7 hydroxyl moiety of a flavonoid and the pyridyl ring of a coformer. Within those species, mutual orientations of molecules as well as flavonoid–coformer stoichiometry and solvent presence in crystal lattice are factors that imply resulting motif formation and crystal packing.

On charge-transfer complexes in the vapor phase

The data on charge-transfer complexes in the vapor phase are analyzed and compared with the data for solutions. An attempt is made to distinguish between the effects of true charge-transfer forces and those attributable to simple van der Waals forces. The complex in the iodine-benzene system in the vapor phase appears to be held together almost solely by van der Waals forces, whereas in other cases the charge-transfer forces contribute in varying degree. Certain inferences are made concerning the mutual orientation of molecules in true charge-transfer complexes, and its effects on the equilibrium constants and absorption intensities. Some remarks on the effect of the complexes on the rate of association of iodine atoms have been appended.

Energy migration as related to the mutual position and orientation of donor and acceptor molecules in LH1 and LH2 antenna complexes of purple bacteria

Many approaches to discovering the interaction energy of molecular transition dipoles use the well-known coefficient xi(phi, psi (1) psi (2)) = (cos phi - 3 cos psi (1) cos psi (2))(2), where phi, Psi (1), and Psi (2) are inter-dipole angles. Unfortunately, this formula often yields rather approximate results, in particular, when it is applied to closely positioned molecules. This problem is of great importance when dealing with energy migration in photosynthetic organisms, because the major part of excitation transfers in their chlorophyllous antenna proceed between closely positioned molecules. In this paper, the authors introduce corrected values of the orientation factor for several types of mutual orientation of molecules exchanging with electronic excitations for realistic ratios of dipole lengths and spacing. The corrected magnitudes of interaction energies of neighboring bacteriochlorophyll molecules in LH2 and LH1 light-absorbing complexes are calculated for the class of photosynthetic purple bacteria. Some advantageous factors are revealed in their mutual positions and orientations in vivo.

What forces can determine the formation of highly specific protein-protein complexes?

A software package was designed and used in a detailed study of the contact regions (interfaces) of a large number of protein-protein complexes using the PDB data. It appeared that for about 75% of the complexes the amino acid composition of the subunit surface in the contact region is not essential. Thus one may suggest that, along with the amino acid residues at the interface, the residues in the interior of the globules substantially contribute to protein-protein recognition. Such interactions between quite remote residues are most probably of electrical nature, and are involved in recognition by contributing to the overall electric field created by the protein molecule; the configuration of this field is perhaps the definitive factor of recognition. The overall field of the protein molecule is additively built of the fields created by each constituent residue, and it can be calculated as a sum of the fields created by the protein multipole (aggregate of 'partial' electric charges assigned to every atom of the protein molecule). Preliminary calculations of the remote electrostatic interaction have been performed for ribonuclease subunits in vacuum. The results are indicative of a real possibility that the electric field created by the protein multipole can strongly influence the mutual orientation of molecules before Brownian collisions.

Calculation of optimal packing and comparison of intermolecular electrostatic interaction models in C60 crystals

Three models of intermolecular interaction potential suggested in the literature for theoretical description of polymorphous transformations in solid fullerene C60 are compared by calculating the optimal packings of molecules. The models are characterized by effective negative charges in the middle of double bonds and opposite charges in the middle of single bonds, at the centers of five-membered rings, or on atoms (this depends on the model). For each model, two packings with different mutual orientations of molecules (I and II), which are present together in a simple cubic Pa3 phase, and several hypothetical packings obtained as potential energy minima are calculated. In the course of energy minimization, six unit cell parameters, Euler angles, and coordinates of the centers of gravity of four independent molecules are varied. It is found that all models correctly predict packing I in a global minimum. For packing II, only the “bond-bond” model is found satisfactory enough. In the case of the “bond-pentagon” model, the molecule is rotated through 25‡ compared to the experiment. This packing is energetically less favorable than the hypothetical monoclinic packing P21/n. In the case of the “bond-atom” model, the minimum of packing II is altogether absent.

Effect of mutual orientation of molecules on kinetics of proton transfer reactions

We calculated the probability of proton transfer within the framework of a two-dimensional model with an arbitrary orientation of the directions of the ruptured and formed bonds. It was shown that the overlap value of the proton wave functions determines the most favorable orientation of the reactants.