[2 + 2] Photodimerization and photopolymerization of diphenylhexatriene crystals utilizing perfluorophenyl-phenyl stacking interactions

Irradiation of the crystal of 1-perfluorophenyl-6-phenyl-1,3,5-hexatriene (1), the 1:1 cocrystal of 1,6-diphenyl-1,3,5-hexatriene (2) and 1,6-bis(perfluorophenyl)-1,3,5-hexatriene (3) (2/3), and crystal 3 gave a mixture of dimer, trimer and higher oligomers that was soluble in common organic solvents. The highest molecular weight was 5000-8000 (the degree of polymerization = 15-20). The order of reactivity was 1 > 2/3 ? 3. The reaction of 1 was relatively efficient compared to typical organic crystals. The conversion reached 100% after 3 h irradiation. In each case, the regio- and stereoselectivity in the photodimerization was high, whereas in the formation of trimer and higher oligomers, the selectivity was much lower. The main dimer was spectroscopically identified to be the face-to-face dimer formed by the [2 + 2] cycloaddition at the 1,2-position of the triene double bonds. The photoproducts from 1 and 2/3 were amorphous, as evidenced by powder X-ray diffraction and polarizing optical microscopy. This is probably due to the nonplanar and bulky structures of the cyclobutane products. The photodimerization and polymerization are considered to be non-topochemical reactions.     

Investigations of the hydrogen bond in the crystals of tropolone and thiotropolone via car-parrinello and path integral molecular dynamics

Car-Parrinello and path integrals molecular dynamics (CPMD and PIMD) simulations were carried out for the 10π-electron aromatic systems: 2-hydroxy-2,4,6-cycloheptatrien-1-one, commonly known as Tropolone (I) and 2-hydroxy-2,4,6-cycloheptatriene-1-thione, called Thiotropolone (II) in vacuo and in the solid state. The extremely fast proton transfer (FPT) and “prototropy” tautomerism in the keto-enol (thione-enethiol) systems have been analyzed on the basis of CPMD and PIMD methods level. Comparisons of two-dimensional (2D) free-energy landscapes of reaction coordinate δ-parameter and R_O…O or R_O…S distances shows that the OH… tautomer to be more favorable in the Thiotropolone. The hydrogen between the oxygen and the sulfur atoms adopts a starkly asymmetrical position in the double potential well. The values of the energy barriers for the FPT were calculated and suggested a strong hydrogen bond with low barrier for FPT mechanism. These studies and the 2D average index of π-delocalization 〈λ〉 landscape of time evolutions of R_O1…O2 and R_C7O2 or R_C7S1 distances for the both crystals indicate that hydrogen bonds in the crystals of Tropolone (I) and Thiotropolone (II) have characteristic properties for the type of bonding model resonance-assisted hydrogen bonds and also low-barrier hydrogen bonds. In the crystal of the Thiotropolone (II), we found the hydrogen bond O H…S existing without the equilibrium of the two tautomers whereas in the crystal of the Tropolone (I) has been confirmed the hydrogen bond O H…O existing with the equilibrium of the two tautomers. It was also found the significant differences in frequency, speed, and the image of the FPT in the studied crystals. © 2018 Wiley Periodicals, Inc.     

Weak interactions involving organic fluorine: a comparative study of the crystal packing in substituted isoquinolines

Weak interactions involving fluorine have been analyzed in the structure of 6-methoxy-1,2-diphenyl-1,2,3,4-tetrahydroisoquinoline with fluorine substitution at para-, meta- and ortho- positions, respectively, on the 1-phenyl ring. The packing modes in the crystalline lattice as determined by X-ray diffraction techniques generate motifs via F?F, C-H?F and C-F?π interactions. The three structures as compared to the parent compound depict conformational changes in the saturated tetrahydroisoquinoline moiety. The salient features of the four structures in terms of weak interactions involving fluorine suggest that organic fluorine does resemble the other halogens.     

Hydrogen-hydrogen bonding: a stabilizing interaction in molecules and crystals

Bond paths linking two bonded hydrogen atoms that bear identical or similar charges are found between the ortho-hydrogen atoms in planar biphenyl, between the hydrogen atoms bonded to the C1-C4 carbon atoms in phenanthrene and other angular polybenzenoids, and between the methyl hydrogen atoms in the cyclobutadiene, tetrahedrane and indacene molecules corseted with tertiary-tetra-butyl groups. It is shown that each such H-H interaction, rather than denoting the presence of "nonbonded steric repulsions", makes a stabilizing contribution of up to 10 kcal mol(-1) to the energy of the molecule in which it occurs. The quantum theory of atoms in molecules-the physics of an open system-demonstrates that while the approach of two bonded hydrogen atoms to a separation less than the sum of their van der Waals radii does result in an increase in the repulsive contributions to their energies, these changes are dominated by an increase in the magnitude of the attractive interaction of the protons with the electron density distribution, and the net result is a stabilizing change in the energy. The surface virial that determines the contribution to the total energy decrease resulting from the formation of the H-H interatomic surface is shown to account for the resulting stability. It is pointed out that H-H interactions must be ubiquitous, their stabilization energies contributing to the sublimation energies of hydrocarbon molecular crystals, as well as solid hydrogen. H-H bonding is shown to be distinct from "dihydrogen bonding", a form of hydrogen bonding with a hydridic hydrogen in the role of the base atom.     

Pure through‐bond state in organic molecules for analysis of the relationship between intramolecular interactions and total energy

Ab initio configuration interaction through‐space/bond interaction analysis was proposed for the examination of specific intramolecular interactions including the effect of electron correlations. To test the effectiveness of our method, we applied it to rotational barrier in ethane. The results of our test suggest that the insensitivity of the ethane barrier to geometric relaxations is intimately connected with the cancellation of interactions through orbital overlaps and other factors. The orbital overlaps include exchange repulsion and hyperconjugation; other factors include classic Coulomb interaction and changes in bond orbital energy. The rotational state without the barrier (pure through‐bond state) can be achieved by deleting not only the “vicinal” interactions between the C? H bonds that belong to different methyl groups but also the “geminal” interactions within the methyl groups. Our mixing analysis of molecular orbitals supports the superiority of the staggered conformer by hyperconjugation. Moreover, it was demonstrated that our treatment could be applied to excited states as well as to the ground state, including electron correlation effects. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem, 2003     

NMR spectra of silatranes and M ← N (M = C, Si, Ge, Sn, Pb) bond lengths in atranes: Substituent effects

The literature data on X substituent influence on the ¹H, ²⁹Si and ¹⁵N NMR chemical shifts (δ) and coupling constants (J) of Si-substituted silatranes , as well as M-N bond lengths (d) in atranes (M = C, Si, Ge, Sn, Pb) have been analyzed. It was established for the first time that the δ, J and d values depend not only on the inductive and resonance effects but also on the polarizability of X substituents. The polarizability contribution ranges from 8% to 25%.     

Typical aromatic noncovalent interactions in proteins: A theoretical study using phenylalanine

A systematic study of CH ··· π, OH ··· π, NH ··· π, and cation ··· π interactions has been done using complexes of phenylalanine in its cationic, anionic, neutral, and zwitterionic forms with CH₄, H₂O, NH₃, and NH at B3LYP, MP2, MPWB1K, and M06‐2X levels of theory. All noncovalent interactions are identified by the presence of bond critical points (bcps) of electron density (ρ( r )) and the values of ρ( r ) showed linear relationship to the binding energies (E_total). The estimated E_total from supermolecule, fragmentation, and ρ( r ) approaches suggest that cation ··· π interactions are in the range of 36 to 46 kcal/mol, whereas OH ··· π, and NH ··· π interactions have comparable strengths of 6 to 27 kcal/mol and CH ··· π interactions are the weakest (0.62–2.55 kcal/mol). Among different forms of phenylalanine, cationic form generally showed the highest noncovalent interactions at all levels of theory. Cooperativity of multiple interactions is analyzed on the basis of ρ( r ) at bcps which suggests that OH ··· π and NH ··· π interactions show positive, whereas CH ··· π and cation ··· π interactions exhibit negative cooperativity with respect to the side chain hydrogen bond interactions. In general, side chain interactions are strengthened as a result of aromatic interaction. Solvation has no significant effect on the overall geometry of the complex though slight weakening of noncovalent interactions by 1–2 kcal/mol is observed. An assessment of the four levels of theory studied herein suggests that both MPWB1K and M06‐2X give better performance for noncovalent interactions. The results also support the fact that B3LYP is inadequate for the study of weak interactions. © 2008 Wiley Periodicals, Inc. J Comput Chem 2009     

Homonuclear chalcogen–chalcogen bond interactions in complexes pairing YO3 and YHX molecules (Y = S,Se; X = H,Cl, Br,CCH, NC,OH, OCH3): Influence of substitution and cooperativity

MP2/aug‐cc‐pVTZ calculations are performed on complexes of YO₃ (Y = S, Se) with a series of electron‐donating chalcogen bases YHX (X = H, Cl, Br, CCH, NC, OH, OCH₃). These complexes are formed through the interaction of a positive electrostatic potential region (π‐hole) on the YO₃ molecule with the negative region in YHX. Interaction energies of the binary O₃Y???YHX complexes are in the range of ?4.37 to ?12.09 kcal/mol. The quantum theory of atoms in molecules and the natural bond orbital analysis were applied to characterize the nature of interactions. It was found that the formation and stability of these binary complexes are ruled mainly by electrostatic effects, although the electron charge transfer from YHX to YO₃ unit also seems to play an important role. In addition, mutual influence between the Y???N and Y???Y interactions is studied in the ternary HCN???O₃Y???YHX complexes. The results indicate that the formation of a Y???N interaction tends to weaken Y???Y bond in the ternary systems. Although the Y???Y interaction is weaker than the Y???N one, however, both types of interactions seem to compete with each other in the HCN???O₃Y???YHX complexes. © 2016 Wiley Periodicals, Inc.     

Intermolecular-medium and intramolecular-weak hydrogen bonding chains in the crystals of chiral trifluoromethylated amino alcohols

A structural feature of hydrogen bonding chains found in the crystals of trifluoromethylated amino alcohols is reported. Hydrogen bondings of 3-(N,N-dialkylamino)-1,1,1-trifluoro-2-propanols construct chiral spiral hydrogen bonding chains. Lone pairs on the nitrogen atoms of the amino alcohols participate in two hydrogen bondings. Detailed structural analysis of the hydrogen bonds of the 3-(N,N-dimethylamino)-1,1,1-trifluoro-2-propanol suggested that the chain built up with alternating intermolecular-medium and intramolecular-weak hydrogen bonds. The medium intermolecular hydrogen bond, which transfers a proton from the hydroxy group to the amino nitrogen, would make a tentative zwitterionic form of the molecule. Then, electrostatic attraction between the charges in the zwitterion centers induced a weak intramolecular hydrogen bond.     

Nature of weak inter- and intramolecular interactions in crystals 4. Bifurcated N—H...N bond in a crystal of 3-amino-6-(3,5-dimethylpyrazol-1-yl)-1,2,4,5-tetrazine

The nature and the energy of the intermolecular bifurcated N—H...N hydrogen bond in the crystal of 3-amino-6-(3,5-dimethylpyrazol-1-yl)-1,2,4,5-tetrazine were studied by analyzing the electron density distribution based on X-ray diffraction data. In contrast to two-center hydrogen bonds, the total energy of the N—H...N interaction is virtually independent of the geometric parameters of two contacts and is determined only by the nature of the interacting atoms. Dedicated to Academician V. I. Minkin on the occasion of his 70th birthday. __________ Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 4, pp. 903–910, April, 2005.     

On the influence of the heterocyclic ring substituents on the structure of dimethylthallium pyrimidine-2-thionato complexes. Crystal structure of dimethyl-(4-trifluoromethylpyrimidine-2-thionate)thallium(III): a compound with intermolecular C-H ? π interactions

The complex [Me₂Tl(4-CF₃pymS)] has been prepared by reacting 4-trifluoromethylpyrimidine-2-thione (4-CF₃pymSH) with dimethylthallium(III) hydroxide in methanol. The resulting compound has a polymeric chain structure, with the thallium atom coordinated by two nitrogen and two sulfur atoms from two different ligands, which act as bridges between two metal atoms, as well as by two carbon atoms of the methyl groups. An intermolecular C-H ? π interaction is observed between an H atom of each methyl group and one of the pyrimidine rings of the neighbouring chain. The structure of the complex is discussed in terms of the IR absorptions, the ¹H, ¹³C and ²⁰⁵Tl NMR spectra and FAB data.     

Assessment of intermolecular interactions at three sites of the arylalkyne in phenylacetylene‐containing lithium‐bonded complexes: Ab initio and QTAIM studies

The intermolecular interactions existing at three different sites between phenylacetylene and LiX (X = OH, NH₂, F, Cl, Br, CN, NC) have been investigated by means of second‐order Møller?Plesset perturbation theory (MP2) calculations and quantum theory of “atoms in molecules” (QTAIM) studies. At each site, the lithium‐bonding interactions with electron‐withdrawing groups (? F, ? Cl, ? Br, ? CN, ? NC) were found to be stronger than those with electron‐donating groups (? OH and ? NH₂). Molecular graphs of C₆H₅C?CH···LiF and πC₆H₅C?CH···LiF show the same connectional positions, and the electron densities at the lithium bond critical points (BCPs) of the πC₆H₅C?CH···LiF complexes are distinctly higher than those of the σC₆H₅C?CH···LiF complexes, indicating that the intermolecular interactions in the C₆H₅C?CH···LiX complexes can be mainly attributed to the π‐type interaction. QTAIM studies have shown that these lithium‐bond interactions display the characteristics of “closed‐shell” noncovalent interactions, and the molecular formation density difference indicates that electron transfer plays an important role in the formation of the lithium bond. For each site, linear relationships have been found between the topological properties at the BCP (the electron density ρ_b, its Laplacian ?²ρ_b, and the eigenvalue λ₃ of the Hessian matrix) and the lithium bond length d(Li‐bond). The shorter the lithium bond length d(Li‐bond), the larger ρ_b, and the stronger the π···Li bond. The shorter d(Li‐bond), the larger ?²ρ_b, and the greater the electrostatic character of the π···Li bond. © 2012 Wiley Periodicals, Inc.     

Role of the hydrogen bond in structural phototransformations of admixture centers in molecular crystals

Structural phototransformations of admixture centers, aniline derivatives in naphthalene crystals, which result in drastic changes in the UV spectra of naphthalene, have been found. The study of the IR spectra suggests that there are admixture aniline derivatives of different types, including those with a hydrogen bond between the amino group of an admixture and -electrons of crystal molecules. Possible arrangements of aniline molecules in naphthalene crystals have been calculated by the method of atom-atomic potentials. The results of the calculation allow one to explain peculiarities of the IR spectra and changes in the UV spectra. The mechanism of structural transformations of admixture centers, which result in cleavage (formation) of the H-bond due to optical excitation (annealing) of the crystal, is suggested.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 7, pp. 1241–1246, July, 1995.     

Nature of weak inter-and intramolecular interactions in crystals 6. Intramolecular O—H...O bond in enol forms of (phosphoryl)acylacetonitriles

The nature of the intramolecular O—H...O bond was studied and its energy was estimated by X-ray diffraction analysis and quantum-chemical calculations (B3LYP/6-311G**) of (diphenylphosphoryl)acylacetonitriles. The influence of the nature of the substituents at the double bond in the H-bonded ring and the crystal packing effects on the hydrogen bond were investigated. Dedicated to Corresponding Member of the Russian Academy of Sciences T. A. Mastryukova. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 11, pp. 2406–2413, November, 2005.     

Polarized IR spectra of the hydrogen bond in acetic acid crystals

The paper presents the results of our investigations of the polarized IR spectra of the hydrogen bond in crystals of acetic acid, CH₃COOH, as well as in crystals of three deuterium isotopomers of the compound: CH₃COOD, CD₃COOH and CD₃COOD. The spectra were measured at 283 K and at 77 K by a transmission method using polarized light. Theoretical analysis of the results concerned the linear dichroic effects, together with the H/D isotopic and temperature effects observed in the solid-state IR spectra of the hydrogen and of the deuterium bond at the frequency ranges of the ν_O–H and the ν_O–D bands, respectively. Basic spectral properties of the crystals can be interpreted satisfactorily in terms of one of the quantitative theories of the IR spectra of the hydrogen bond, i.e. the “strong-coupling” theory or the “relaxation” theory when a hydrogen bond dimer model is used. From the spectra obtained it resulted that the strongest exciton coupling involved the closely spaced hydrogen bonds, belonging to different chains of associated acetic acid molecules. These results contradict the former explanation of the spectra within a model, which assumed a strong vibrational exciton coupling between four hydrogen bonds in a unit cell. On analyzing the spectra of isotopically diluted crystalline samples of acetic acid it has been proved that a non-random distribution of the protons and deuterons takes place in the hydrogen bond lattices. This non-conventional isotopic effect is a result of dynamical co-operative interactions involving hydrogen bonds in the system. Simultaneously it has been also found that in an individual hydrogen bonded chain in the crystals, distribution of the hydrogen isotope atoms H and D was fully random. The H/D isotopic “self-organization” mechanism most probably involves a pair of hydrogen bonds from each unit cell where each hydrogen bond belongs to a different chain.     

New angle‐dependent potential energy function for backbone–backbone hydrogen bond in protein–protein interactions

Backbone–backbone hydrogen bonds (BBHBs) are one of the most abundant interactions at the interface of protein–protein complex. Here, we propose an angle‐dependent potential energy function for BBHB based on density functional theory (DFT) calculations and the operation of a genetic algorithm to find the optimal parameters in the potential energy function. The angular part of the energy funtion is assumed to be the product of the power series of sine and cosine functions with respect to the two angles associated with BBHB. Two radial functions are taken into account in this study: Morse and Leonard‐Jones 12‐10 potential functions. Of these two functions under consideration, the former is found to be more accurate than the latter in terms of predicting the binding energies obtained from DFT calculations. The new HB potential function also compares well with the knowledge‐based potential derived by applying Boltzmann statistics for a variety of protein–protein complexes in protein data bank. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010     

A method for determination of the structure of the intramolecular hydrogen bond in the cations of unsymmetrically substituted 1,8-bis(dimethylamino)naphthalenes in solution

Alkylation of 8-dimethylamino-1-methylamino-4-nitronaphthalene in the CD₃I/KOH/DMSO system afforded a 4-nitro derivative containing the N(CD₃)Me group in position 1. Direct proof of the structure of the intramolecular hydrogen bond in solutions of monoprotonated 4-R-1,8-bis(dimethylamino)naphthalenes was obtained for the first time. ¹H NMR study revealed that the chelated NH proton is shifted to the N(8) atom for R = NO₂ and NH₃ ⁺ and to the N(1) atom for R = NH₂. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 1, pp. 159–162, January, 2006.