Solvent effects on the nπ* transition of pyrimidine in aqueous solution

A hybrid quantum mechanical and molecular mechanical potential is used in Monte Carlo simulations to examine the solvent effects on the electronic excitation energy for the n→π* transition of pyrimidine in aqueous solution. In the present study, the pyrimidine molecule is described by the semi-empirical AM1 model, while the solvent molecules are treated classically. Two sets of calculations are performed: the first involves the use of the pairwise three-point charge TIP3P model for water, and the second computation employs a polarizable many-body potential for the solvent. The latter calculation takes into account the effect of solvent polarization following the solute electronic excitation, and makes a correction to the energies determined using pairwise potentials, which neglects such fast polarization effects and overestimates the solute-solvent interactions on the Franck-Condon excited states. Our simulation studies of pyrimidine in water indicate that the solvent charge redistribution following the solute electronic excitation makes modest corrections (about −130␣cm⁻¹) to the energy predicted by using pairwise potentials. Specific hydrogen bonding interactions between pyrimidine and water are important for the prediction of solvatochromic shifts for pyrimidine. The computed n→π* blue shift is 2275±110 cm⁻¹, which may be compared with the experimental value (2700 cm⁻¹) from isooctane to water. Received: 14 January 1997 / Accepted: 21 February 1997     

Bioisosteric equivalence of five-membered heterocycles

A variety of factors can affect bioisosteric relationships between structural motifs in a medicinal chemistry optimization project, both in terms of ligand affinity to a given target and off-target profile. Such parameters, e.g. the ability to participate in hydrogen bonding and π–π interactions, basicity, and solubility are discussed with a particular focus on five-membered heterocycles and their application in drug design.     

Hydrogen bonding interactions between <Emphasis Type="Italic">N</Emphasis>,<Emphasis Type="Italic">N</Emphasis>-dimethylformamide and cysteine: DFT studies of structures,properties, and topologies

The hydrogen bonding interactions between cysteine and N,N-dimethylformamide (DMF) were studied at the extended hybrid functional DFT-X3LYP/6-311++G(d,p) level regarding their geometries, energies, vibrational frequencies, and topological features of the electron density. The quantum theory of atoms in molecules (QTAIM) and natural bond orbital (NBO) analyses were employed to elucidate the interaction characteristics in the complexes. The results show that two intermolecular hydrogen bonds (H-bonds) are formed in one complex except few complexes with one intermolecular H-bond. The H-bonds involving O atom of DMF as H-bond acceptor usually are red-shifting H-bonds, while the blue-shifting H-bond usually involve methyl of DMF or methenyl of cysteine moiety as H-bond donors. Both hydrogen bonding interaction and structural deformation play important roles in the relative stabilities of the complexes. Due to the π-bond cooperativity, the strongest H-bond is formed between hydroxyl of cysteine moiety and O atom of DMF, however, the serious deformation counteract the hydrogen bonding interaction to a great extent. The complex involves a stronger hydrogen bonding interaction as well as the smaller deformation is the most stable one. The electron density (ρ_b) as well as its Laplacian (∇²ρ_b) at the H-bond critical point predicted by QTAIM is strongly correlated with the H-bond structural parameter (δR _H···Y) and the second-perturbation energies E(2) in the NBO scheme.     

Self-diffusion of water and alkaline cations in bisulfur-containing aromatic polyamides-water systems

Aromatic copolyamides based on diamino sulfoacids, unsubstituted aromatic diamines, and phthalyl dichlorides were synthesized. Self-diffusion of water and alkaline cations in aqueous Li⁺, Na⁺, and Cs⁺ salts of the iso-polymer (μPA) and Li⁺ salt of the tere-polymer (πPA) of aromatic bisulfur-containing polyamides was studied by NMR with a magnetic field pulse gradient. A supramolecular structure was formed by hydrogen bonding between the carbonyl and N-H groups of adjacent macromolecules with two water molecules included in them as structure-forming bridges. The oversorbed water was incorporated in the ionogen channels formed by the sulfo groups, counterions, and water molecules. The conclusion was drawn that the structure of ionogen channels was more regular in πPA than μPA. The self-diffusion coefficients of metal cations increase in the series Li < Na < Cs.     

Novel type of mixed O–H···N/O–H···π hydrogen bonds: monohydrate of pyridine

Investigation of characteristics of hydrogen bonding between pyridine and water by MP2/aug-cc-pvdz method reveals that these two molecules may form three types of hydrogen bonds depending on nature of proton withdrawal site of pyridine. Change of orientation of water with respect to plane of aromatic ring leads to transformation of the O–H···N bond to O–H···π bond via wide region of the potential energy surface where both lone pair of the nitrogen atom and π-system make significant contribution into hydrogen bonding. Hydrogen bond in this intermediate region may be considered as mixed O–H···N/O–H···π bond representing new type of H bonds.     

Exploration of conformations and quantum chemical investigation of l-tyrosine dimers, anions, cations and zwitterions: a DFT study

Conformational analysis of tyrosine (YN) and its ionized counter parts cations (YC), anions (YA) and biologically relevant zwitterionic form (YZ) has been carried out. An exhaustive and systematic exploration of l-tyrosine dimer (YD) conformations resulted in about 59 distinct minima on the potential energy surface. The hydrogen bonds and a variety of non-covalent interactions such as OH–π, NH–π, CH–π, CH–O and π–π interactions stabilized the different forms of tyrosine and its dimers. Atoms in molecules analysis was performed to evaluate the nature and strength of the non-covalent interactions. Over all the NH–O, hydrogen bonds have showed higher stability than other non-covalent interactions in this study. The most stable dimers predominantly possess hydrogen bonding interactions, while the ones with aromatic side chain interactions are less stable. A delicate balance of non-covalent interactions governed the stability of different forms of tyrosine and its dimers.     

Features of atomic interaction in the molecules of furan, pyrrole, and their 2-chlorine-substituted derivatives according to results ofab initio calculations

The results of abinitio studies by the RHF/6-31G(d) method on the molecules of furan, pyrrole, and their 2-chlorine-substituted derivatives with full optimization of the geometry show thatunshared electron pairs of their heteroatoms are not delocalized solely in the π-system of the heterocycle. The participation of these electron pairs in formation of bonding and other MOs does not make it possible to speak of substantial role for p,π-conjugation in the distribution of electron density in the molecules and its effect on the characteristics of thecompounds. The results of the ab initio calculations were used to determine the³⁵Cl NQR parameters of the 2-chlorine-substituted molecules. Institute of Technical Chemistry, Urals Branch, Russian Academy of Sciences, Perm'. Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 5, pp. 612–617, May, 1999.     

Mechanism of enantioseparation on zeolite-supported chiral stationary phases in the presence of lipophilic buffer

Summary Chiral stationary phases have been prepared on a zeolite A support. In addition to polar hydrophilic chiral selector molecules derived from DNB-L-Leu and DNB-L-Phe amides, dynamic modification of the underivatized free surface hydroxyl (silanol) groups of the zeolite can be used to increase the overall hydrophobic character. On these non-capped chiral stationary phases, in the presence of lipophilic buffer salts in the aqueous organic phase, the enantioseparation of ion-paired D,L-mandelic acid was facilitated and was studied in more detail. The enantioseparation might be based on hydrogen bonding and π-π interaction supported by simultaneous hydrophobic interaction. Presented at: Balaton Symposium on High-Performance Separation Methods, Siófok, Hungary, September 3–5, 1997.     

Glycoprotein adsorption into bilirubin/cholesterol mixed monolayers at the air-water interface

The adsorption of α₁-acid glycoprotein into bilirubin/cholesterol mixed monolayers with various component molar ratios is investigated using surface pressure-area (π-A) isotherms and (dπ/dA)-A curves. The results showed that the surface area per molecule increased after the adsorption/insertion of glycoprotein molecules into the monolayers. The compressibility of mixed monolayers increased as a result of hydrogen bonding between bilirubin and glycoprotein molecules, while the interactions between bilirubin and cholesterol are weakened. The adsorption of glycoprotein into a monolayer induced changes in molecular surface area depending on the surface pressure and molar fraction of bilirubin. The transmission electron microscopy of mixed monolayers confirmed the insertion of glycoprotein particles of spherical shape with an average diameter of about 80 nm into the monolayer. The text was submitted by the authors in English.     

A simple procedure for estimating changes in the nuclear configuration of molecules in the excited ππ*-electronic state

A simple procedure is suggested for estimating changes in the bond lengths q and angles a between them in the excited ππ states of molecules avoiding calculations of molecular vibrations. The distances q and the angles a are estimated for the triplet state B_1u (ππ*) of the tetm-β-chlomdioxin molecule. Translated from Zhumal Struktumoi Khimii, Vol. 41, No. 1, pp. 149-156, January–February, 2000.     

Ab-initio SCF study of the nature of bonding in neutral and cationic silicon hydrides and analogous carbon compounds

The nature of bonding in a number of neutral and cationic silicon hydrides has been studied on the basis of atomic charge (q_A), valency (V_A), molecular valency (V_M) and localised molecular orbitals (LMO). Several structural isomers of each species have been considered. It is found that the most stable isomer is generally associated with maximum q_si and minimum V_si and V_M. Protonation of the neutral hydrides leads to an increase in the positive charge of Si, and in molecular valency. The bonding characteristics of the most stable isomers of the silicon hydrides have been compared with that of analogous hydrocarbons. It has been observed that the difference in bonding stems mainly from the highly electro-positive nature of the Si atom which prefers to form three-centre rather than multiple bonds. The molecular hardness parameters (η) have also been calculated. The most stable isomers of silicon hydrides are generally associated with maximum η. The HSAB principle has been tested by considering some hydrogenation and proton transfer reactions. It is qualitatively satisfied in both cases.     

A covalent attraction between two molecular cation TTF·+

The optimized structure of the tetrathiafulvalence radical-cation dimer (TTF·⁺-TTF·⁺) with all-real frequencies is obtained at MP2/6-311G level, which exhibits the attraction between two molecular cation TTF·⁺. The new attraction interaction is a 20-center-2-electron intermolecular covalent π/π bonding with a telescope shape. The covalent π/π bonding has the bonding energy of about −21 kcal·mol⁻¹ and is concealed by the Coulombic repulsion between two TTF·⁺ cations. This intermolecular covalent attraction also influences the structure of the TTF·⁺ subunit, i.e., its molecular plane is bent by an angle θ = 5.6°. This work provides new knowledge on intermolecular interaction.     

Synthesis and crystal structure of a new Cd(II) coordination polymer with mixed Oba and TATP ligands (H<Subscript>2</Subscript>Oba = 4,4′-oxybis(benzoic acid), TATP = 1,4,8,9-tetranitrogen-trisphene)

A new coordination polymer, [Cd(Oba)(TATP) · H₂O(I) (Oba = anion of 4,4′-oxybis(benzoic acid), TATP = 1,4,8,9-tetranitrogen-trisphene), has been solvothermally synthesized and structurally characterized by IR, elemental analysis, and single crystal X-ray diffraction. Single-crystal X-ray diffraction reveals that I is an interesting 1D zigzag chain structure. The adjacent chains are further connected together via the strong π−π packing interactions and hydrogen bonding to form a 3D supramolecular framework.     

Conjugation in radical cations of benzene, ethylene, and acetylene derivatives. Nonuniversality of the resonance parameters of group 14 organoelement substituents

The first vertical ionization potentialsl ₁ of molecules R_πX (X=Ph, H₂C=CH, and HC≡C) depend on the joint influence of the inductive, resonance, and polarizability effects of substituents X, which are characterized by parameters σ₁, σ_R+, and σ_α, respectively. The mechanism of conjugation in radical cations formed upon ionization of R_πX is changed as compared to neutral R_πX molecules, while the substituent X becomes polarized. The conjugation and polarizability effects are strenthened in the sequence Ph < H₂C=CH <HC≡C as R_π changes from Ph to H₂C=CH and HC≡C. The σ_R+ parameters of Si-, Ge-, and Sn-containing substituents X are dependent on the type of R_π but are connected by linear dependences in the series of benzene, ethylene, and acetylene derivatives. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 8, pp. 1481–1486, August, 1998.     

Density functional study on zerovalent lanthanide bis(arene)-sandwich complexes

Several zerovalent lanthanide bis(arene)-sandwich complexes, Ln(η⁶-C₆H₆)₂, Ln = La, Ce, Eu, Gd and Lu, have been studied by means of density functional theory. The calculated geometries are in good agreement with experiment. The calculated dissociation energies of the bond Ln-(η⁶-C₆H₆) may be considerably underestimated, but they correctly reveal the variation regularity. The bonding in these molecules can be described in terms of a relatively weak π-electron donation from benzene to Ln and a stronger electron back-donation from Ln 5d to the benzene π* orbitals. During bond formation, there is electron promotion from Ln 6s to 5d instead of from 4f to 5d, in opposition to the proposal of Anderson et al. The relativistic effect only slightly influences the molecular geometry, but decreases the bonding energy considerably through lowering the Ln 6s level and raising the 5d level. It enhances the trend of the bonding energy to decrease along the lanthanide series. Received: 22 June 1998 / Accepted: 9 September 1998 / Published online: 17 December 1998     

CEPA calculations on open-shell molecules. II. Singlet-triplet energy splitting in π2 configurations of diatomic molecules

The CEPA-PNO method is used for calculating the energy difference ΔE _ST between the³∑⁻ and the¹Δ states of diatomic molecules in electronic π² configurations. An analysis of the contribution of electron correlation to ΔE _ST is performed in terms of physically understandable effects such as direct correlation, dynamic spin polarization, semiinternal and internal excitations. It is shown that these effects are of completely different importance for the molecules treated in this study: For C₂ the direct correlation between the two singly occupied π-orbitals is the dominant correlation contribution to ΔE _ST; for O₂, S₂, SO the internal excitation π _u ² → π _g ² is predominant, whereas for NH and PH there is a close competition between the direct correlation and the spin polarization of the underlying σ-orbitals. The basis set dependence of these effects is investigated, in particular for NH. Our final results reproduce experimental values of ΔE _ST within 0.05–0.10 eV.     

Revisiting superdelocalizability. Mathematical stability of reactivity indices

Superdelocalizability, S _r, defined by Fukui et al. as a variant of reactivity indices in the Hückel molecular orbital scheme for conjugated hydrocarbon molecules is reinvestigated with particular emphasis on its behavior for infinitely large π-electronic systems. Surprisingly, almost all the S _r values of polyacetylene are found to diverge with the size of molecule, while all the S _r values of comb polyene converge to certain values. Similarly, the S _r values of linear polyacene diverge, while those of zigzag polyacene converge. Whether the superdelocalizability for a series of periodic polymers converges or diverges can be predicted, respectively, if the density of states of the infinitely large π-electron network is shown to have non-zero or zero gap at the Fermi level. The behavior of atom-atom polarizability defined by Coulson et al. is also checked and discussed. Received: 27 July 1998 / Accepted: 9 September 1998 / Published online: 23 February 1999     

Crystal structure of hinokiol isolated from <Emphasis Type="Italic">Isodon henryi</Emphasis>

Hinokiol was isolated for the first time from Isodon henryi and the structure was elucidated on the basis of IR and NMR spectra analysis. Its molecular configuration, conformation, and crystal structure were also characterized by X-ray structure analysis. The infrequent H-π stacking and hydrogen bonding assemble the molecules of hinokiol into a three-dimensional network structure. Published in Khimiya Prirodnykh Soedinenii, No. 3, pp. 229–230, May–June, 2007.     

Binding affinities and spectra of complexes formed by dehydrotetrapyrido[20]annulene and small molecules

Theoretical study on the binding affinities of dehydrotetrapyrido[20] annulene to the alkene and aromatic molecules was performed using the AM1 and DFT methods. It indicated that the host possesses the ability to bind the above molecules since the binding energies of the complexes were negative. The complexes were stabilized via the hydrogen bonding, static effect, and π — π stacking interaction between the host and guest molecules. Based on the B3LYP/3-21G optimized geometries, the electronic, IR, and NMR spectra were calculated using the INDO/CIS, AM1, and B3LYP/3-21G methods, respectively. Due to the hydrogen bonding, the first absorption maxima in the electronic spectra of studied complexes were blue-shifted, whereas the main IR frequencies for some of the complexes were red-shifted. At the same time, the chemical shifts of carbon atoms forming the bonds in the complexes were lower, compared to those of the host.     

Influence of the out-of-plane distortions of nuclear configurations of molecules with then-AO of the heteroatom directed along theC 2 symmetry axis on spin-orbit coupling between thenπ*- and ππ*-states

This paper studies changes in the matrix elements (U_mp) of spin-orbit coupling between the nπ^*- and ππ^*-states, which are induced by the (“chair,” “bath”) distortions of the nuclear configurations of molecules. The analysis is performed for acridine molecules in which the n-p_z atomic orbital (AO) of the heteroatom is directed along the C₂ symmetry axis. Earlier, for molecules with a planar nuclear configuration of C_2v symmetry and with the heteroatom lying on the C₂ axis, we established the dependence of U_mp on the symmetry of ππ^*-states [Γ(ππ^*)=A₁ or B₂]. The values of U_mp differ by more than one order of magnitude; this is in line with the difference between the interconversion rate constants (K_isc; two or three orders). In this work we have found that this contrast in U_mp (and, accordingly, in K_isc) is retained when the nuclear configuration of the acridine molecule is distorted to the “chair” (AC-A) configuration, although the individuality of both molecular orbital types (nσ-MO and π-MO) and states nπ^* and ππ^* is annihilated to a certain extent. For the “bath” (AC-B) conformation the difference in U_mp considerably diminishes. Reasons for the changes in the matrix elements of spin-orbit coupling and rate constants of the S-T conversion are analyzed. The available energy level diagram is critically analyzed, and a slightly different diagam as well as a scheme of nonradiating deactivation of acridine are suggested. L. Ya. Karpov Physicochemical Scientific Research Institute. Translated fromZhurnal Strukturnoi Khimii, Vol. 36, No. 2, pp. 292–297, March–April, 1995. Translated by L. Smolina