A pseudopotential study of the hydrogen bond in H2O·H2S,H2S·H2S and H2O·H2Se systems

Intermolecular potential energy curves for the hydrogen bonded systems H₂O·H₂S, H₂O·H₂Se and H₂S·H₂S were calculated with nonempirical pseudopotentials using optimized-in-molecules basis sets augmented by polarization functions. The H₂O·H₂O interaction energy curve has been also considered as a test case. The present results for H₂O·H₂S and H₂S·H₂S indicate much weaker intermolecular interactions than those found in previous ab initio calculations. The H₂O·H₂Se interaction was found to be quite similar to H₂O·H₂S.This work was partly supported by the Polish Academy of Sciences within the Project PAN-09, 7.1.1.1On leave from Quantum Chemistry Laboratory, Dept. of Chemistry, University of Warsaw, Pasteura 1, 02-093. Warsaw, Poland     

Electrochemical behavior of fullerene C60 and substituted fullerenes immobilized on an electrode surface

The effect of substituents with different donor capabilities, which are inserted into a molecule of fullerene C₆₀, on the kinetics and thermodynamics of redox conversions of fullerenes that are immobilized on an electrode, is studied for the first time. To this end, redox conversions that occur with rubbed-on films of fullerene and fulleropyrrolidines are studied using cyclic voltammetry in 0.5 M KCl/H₂O and a 0.1 M (C₄H₉)₄NBF₄/AN solution in acetonitrile. A hypothesis that the kinetics of redox conversions occurring with films of individual fullerenes is defined largely by changes in the structure of initial films in the process of their cathodic doping is used. The effect of the substituents is explained in the framework of this hypothesis by a transition from a dense crystalline structure of nonsubstituted fullerene C₆₀ to an amorphous structure of substituted fullerenes. It is demonstrated that the formal potentials corresponding to redox conversions of fullerenes in a solid cationic lipid matrix are defined by the energy of interaction of anions, which are products of reduction of fullerenes, with cations of the matrix. As a result of this interaction, the formal potentials of the process of cathodic doping shift to less negative values. It is established that the insertion of a donor substituent and increase in its donor capability amplify the energy of interaction of the fullerene anions with the lipid cations.     

A theoretical study of the relative affinities of an aliphatic and an aromatic bisguanylhydrazone for the minor groove of double-stranded (dA-dT) n oligomers

The nonintercalative binding of an aliphatic and an aromatic bisguanylhydrazone (BGH) to the minor groove of double-stranded (dA-dT) _n oligomers is investigated by means of theoretical computations. The preferred binding arrangements of both BGHs are stabilized by a number of H-bonding interactions with sites O₂(T), N₃(A) and o₁ on the two strands, and require limited conformational rearrangements of the BGHs around their C-C single bonds. The intermolecular interaction energy is larger with the aliphatic BGH than with the aromatic one. The energy difference is, however, considerably reduced when the oligomer is lengthened: it passes from 16.1 kcal/mole at the heptamer level, to 7.9 kcal/mole at the undecamer level and to 4.6 kcal/mole when each strand of the undecamer is flanked with a complementary complete helical turn of phosphates, on both the 3 and 5 termini.The interaction energies of the BGHs with water molecules in the first hydration shell are, however, also larger with the aliphatic BGH, than with the aromatic BGH. This energy difference is further enhanced when one considers also the water molecules in the second shell. It becomes greater than the difference in the interaction energy of the two BGHs with (dA-dT) _n for large values of n. When the dehydration energy of BGHs is taken into account the overall energy balance is then more favorable for the interaction of the aromatic than of the aliphatic BGH with the polynucleotide. This last conclusion is in agreement with experimental results.     

A theory of molecules in molecules IV. Application to the Hydrogen Bonding Interaction in NH3 · H2O

The theory of molecules in molecules introduced in previous articles is applied to study the hydrogen bonding interaction between an ammonia molecule as proton acceptor and a water molecule as proton donor. The localized orbitals which are assumed to be least affected by the formation of the hydrogen bond are transferred unaltered from calculations on the fragments NH₃ and H₂O, the remaining orbitals are recalculated. A projection operator is used to obtain orthogonality to the transferred orbitals. Additional approximations have been introduced in order to be able to save computational time. These approximations can be justified and are seen to lead to binding energies and bond lengths which are in satisfactory agreement with the SCF values. The point charge approximation for the calculation of the interaction energy between the two sets of transferred localized orbitals is, however, not applicable in this case. An energy analysis of the effect of the hydrogen bond on the localized orbitals of the two fragments is given.     

The influence of layer curvature on switching in ferroelectric B2 phases of liquid crystals having bent-shape molecules

In the B₂ phase of liquid crystalline compounds with bent-shape molecules ferroelectric switching can occur either by molecular rotation on the cone or by rotation of the molecule about its long axis (so-called chirality flipping), or by both mechanisms simultaneously. When the smectic layers of the B₂ phase are non-deformed and parallel the rotation of molecules under an external electric field occurs readily on the surface of the cone, while rotation around the long molecular axis is hindered by an energy barrier. Imposed deformation of smectic layers leads to interaction between local layer curvatures and molecular orientation, which results in the energy barrier hindering the molecular rotation by a cone. For appropriate constants describing this interaction the energy barrier can be so high that chirality flipping becomes the principal switching mode. An increase in the electric field can eliminate layer curvature, and therefore the energy barrier, so that switching with molecular rotation on the cone becomes possible. In the present contribution these mechanisms of switching are discussed and the influence of layer curvature on the switching mode is demonstrated.     

Theoretical study of the solvation of nitrogen. Two different approaches

Two different approaches were used for a theoretical study of the solvation of N₂, with HF, H₂O, NH₃, CH₄ as solvents. In the first approach, the contour maps of orientationally optimized interaction energy between N₂ and one solvent molecule were computed by fast semiempirical methods (Extended Hückel and CNDO/2) in order to find a reliable but not too expensive calculation method for solvation models. In the case of the N₂-H₂O system, anab initio map was also evaluated for comparison. The second approach is based on the building up of clusters with one molecule of N₂ surrounded by a number (2 to 8) of solvent molecules and finding the structure of such clusters by energy minimization. From the structures obtained it results that they are determined mainly by steric factors, so that clusters optimized by means of different methods are similar, despite the remarkable differences in the maps.     

Interaction of colloidal TiO2 with bovine serum albumin: A fluorescence quenching study

The interaction between colloidal TiO₂ and bovine serum albumin (BSA) was studied by using absorption and fluorescence spectroscopic methods. The quenching of the intrinsic protein fluorescence in the presence of different concentrations of colloidal TiO₂ was analyzed and number of binding sites (n) and apparent binding constant (K) were measured. The quenching mechanism of albumin by colloidal TiO₂ is discussed. The energy transfer efficiency (E) and critical transfer distance (R₀) were determined.     

A fully ab initio potential energy surface for ClH2 reactive system

Anab initio analytical potential energy surface called BW3 for the ClH₂ reactive system is presented. The fit of this surface is based on about 1 200ab initio energy points, computed with multi-reference configuration interaction(MRCI) and scaling external correlation (SEC) method and a very large basis set. The precision in the fit is very high. The BW3 surface could reproduce correctly the dissociation energy of H₂ and HCl, and the endothermicity of the Cl + H₂ abstraction reaction. For the Cl + H₂ abstraction reaction, the saddle point of BW3 lies in collinear geometries, and the barrier height is 32.84 kJ/mol; for the H + ClH exchange reaction, the barrier of BW3 is also linear, with a height of 77.40 kJ/mol.     

Role of ammonium ions on the stability of TiO2 sol

In this paper, the role of the trace ammonium ions on the stability of TiO₂ sol prepared by peroxo titanic acid (PTA) sol was investigated. The results showed that the removal of ammonium ions in PTA sol is beneficial to reduce agglomeration and increase the negative charge on the surface of TiO₂ colloidal particles, contributing to the higher stability and longer storage time of the TiO₂ sol. It was also approved by the increase of interaction energy calculated by classical DLVO theory. In addition, the photocatalytic performance of TiO₂ sol was improved due to the decrease of aggregation of TiO₂ colloidal particles.     

Impact of electron-electron interaction on the electron energy distribution function in molecular plasmas under rf field action

Calculations of the electron energy distribution and of relevant macroscopic quantities of collision-dominated, weakly ionized plasmas under rf field action have been performed with increasing degrees of ionization, and the impact of the electron-electron interaction on these quantities was determined. The investigations were performed for the gas plasmas in CO and H₂ as representatives of molecular plasmas The energy distribution and macroscopic quantities are obtained by solving the nonstationary Bolizmann equation for a given rf field and degree of ionization taking into accoung and additional Fokker-Planck term besides the collision integrals for the elastic and the main inelastic collision processes. In these molecular plasmas a remarkable impact of the electron-electron interaction connected with increasing Maxwellization is observed for degrees of ionization greater than 10.     

稀土掺杂Lu3Al5O12荧光粉的发光特性及能量传递

采用高温固相法制备了Ce、Sm共掺Lu_3Al_5O_(12)荧光粉。通过X射线衍射分析、荧光光谱分析研究了样品的结构、发光特性,并通过理论计算研究了能量传递效率、能量传递的临界距离以及能量传递方式。X射线衍射分析表明所制备的荧光粉具有单一的石榴石结构;荧光光谱分析表明,在464 nm蓝光激发下,Sm~(3+)的引入可增加Lu_3Al_5O_(12)∶Ce,Sm发射光谱中红光成分,并且随着Sm~(3+)浓度的增加,Ce~(3+)发光强度逐渐减弱。计算出Ce~(3+)、Sm~(3+)之间的能量传递效率高达77.42%,确定了Ce~(3+)、Sm~(3+)之间的能量传递机制为偶极-偶极相互作用。     

金红石TiO2纳米团簇与铀酰相互作用的相对论密度泛函理论计算

采用全电子相对论密度泛函理论方法探索金红石型Ti O_2纳米团簇与铀酰的相互作用。考察金红石团簇模型(包括层数和表面积大小)变化对吸附铀形成复合物结构、吸附作用能等性质的影响,确定2层、表面积为1.1 nm×0.6 nm、包括63个原子的纳米团簇(标记为2L-Ti15)能够合理描述金红石纳米粒子性质的同时,还能节约计算资源。对2L-Ti15-[(UO_2)(H_2O)_3]~(2+)复合物计算表明,纳米团簇和铀酰存在共价键作用;优化得到U-O_(surf)键长0.233~0.238 nm,这一距离在已发现铀酰基配合物U-O距离范围内。在气相条件下,纳米团簇对铀酰吸附反应为放热过程(-3.02 e V);考虑溶剂介质环境的影响,反应则需要吸收少许能量(0.16e V)。U-O_(surf)键的能量分解发现,纳米团簇和铀酰的化学键作用为轨道相互作用主导的(占94%),它的静电吸引略大于Pauli排斥。基于电子密度的QTAIM(quantum theory of atoms in molecule)分析揭示,U-O_(surf)作用是介于离子和共价之间的配位键,其强度高于复合物中的U-OH_2键作用,但比U=O键弱。波函数分析表明,来自纳米团簇的O(2p)贡献HOMO轨道,并混有σ(U=O)成键性质,而LUMO轨道则为Ti(3d)修饰的U(5f)性质,复合物HOMO-LUMO带隙为2.40 e V,相对吸附前的纳米团簇半导体粒子的3.35 e V变窄。从吸收光谱角度而言,复合物体系可能在可见光区域具有更强的捕光性能。     

An ab initio study of O2 and CO2 transport by perfluorocarbons

Fluorocarbons have been successfully applied as oxygen carriers replacing blood. In order to understand the nature of the interaction between fluorocarbons and hydrocarbons on the one hand and O₂, N₂ and CO₂ on the other, STO-3G calculations have been performed on their complexes. The very slight energies of interaction that were obtained seem to substantiate the contention that O₂, N₂ and CO₂ are physically dissolved in fluorocarbons. This energy of interaction is, however, distinctly larger for fluorocarbons than for hydrocarbons. Electrostatic potentials have been computed around several fluorocarbons. They make it possible to predict the geometries of the complexes that are formed.     

First-principles study of O2 adsorption and dissociation on the CuCr2O4 (100) surface

The adsorption and dissociation of molecular oxygen on spinel CuCr₂O₄ (100) surface were carried out by first-principles calculations based on density functional theory (DFT). The calculated results indicate that the Cr site is most favorable for atomic oxygen adsorption, with an adsorption energy of 402.8 kJ/mol. For molecular oxygen adsorption, there are three types of favorable interaction modes: O₂ forms bonds with the Cu site or O₂ binds to two Cr sites or O₂ interacts with both Cu and Cr sites simultaneously. The lowest activation energy (E_a = 35.4 kJ/mol) was found through exploring possible reaction pathways for O₂ dissociation. The relationship between E_a and reaction enthalpy (ΔH) for O₂ dissociation adsorption reactions fits Brønsted-Evans-Polanyi (BEP) behavior.     

The C2H 3 + cation and its interaction with HF

The structure and stability of classical and bridged C₂H ₃ ⁺ is reinvestigated. The SCF and CEPA-PNO computations performed with flexibles andp basis sets including twod-sets on carbon confirm our previous results. We find the protonated acetylene structure to be more stable than the vinyl cation by 3.5–4 kcal/mol. The energy barrier for the interconversion of these two structures is at most a few tenths of a kcal/mol. The equilibrium SCF geometries of Weberet al. [15] are affected insignificantly by further optimization at the CEPA-PNO level. Several structures for the interaction of C₂H ₃ ⁺ with HF have been investigated at the SCF level. With our largest basis set which includes a complete set of polarization functions we find a remarkable levelling of the stabilities of most of the structures. In these cases the stabilization energy ΔE ranges from −10 to −13 kcal/mol.     

Model studies on the interactions of a Cu(II)-quinone complex with surfactant micelles and DNA explore its induction of apoptosis in human MDA-MB-231 breast adenocarcinoma cells

The interactions of copper complex (CuQ₂) of 1-amino-4-hydroxy-9,10-anthraquinone (QH) with calf thymus DNA, anionic surfactant sodium dodecyl sulfate (SDS), and cationic surfactant cetyltrimethylammonium bromide (CTAB) were investigated in an aqueous solution at physiological pH (7.4). Affinities of such molecule to DNA and surfactant micelles, a model for a biological membrane, are important in determining its biological action. Using different models, various binding parameters were evaluated in both of molecule–DNA interaction and molecule–surfactant interaction. The study showed that hydrophobic interaction plays a major role in the binding of CuQ₂ to surfactant micelles. In addition, the hydrophobic interaction has an important role in the distribution of CuQ₂ between micelle-water phases. Gibbs free energy for the binding and distribution of CuQ₂ between the bulk aqueous medium and surfactant micelles were calculated. In order to correlate the physicochemical properties deciphered from the aforementioned studies with the biological property of the molecule, CuQ₂ was treated with MDA-MB-231 breast adenocarcinoma cells where it was found that the molecule affects the viability of the cancer cells. Fluorescent staining of the treated cells with AO/EB and Hoechst indicated that the CuQ₂ induces apoptosis, suggesting its use in the treatment of breast cancer.     

Modelling and mutation studies on the histamine H1-receptor agonist binding site reveal different binding modes for H1-agonists: Asp116 (TM3) has a constitutive role in receptor stimulation

Summary A modelling study has been carried out, investigating the binding of histamine (Hist), 2-methylhistamine (2-MeHist) and 2-phenylhistamine (2-PhHist) at two postulated agonistic binding sites on transmembrane domain 5 (TM5) of the histamine H₁-receptor. For this purpose a conformational analysis study was performed on three particular residues of TM5, i.e., Lys²⁰⁰, Thr²⁰³ and Asn²⁰⁷, for which a functional role in binding has been proposed. The most favourable results were obtained for the interaction between Hist and the Lys²⁰⁰/Asn²⁰⁷ pair. Therefore, Lys²⁰⁰ was subsequently mutated and converted to an alanine, resulting in a 50-fold decrease of H₁-receptor stimulation by histamine. Altogether, the data suggest that the Lys²⁰⁰/Asn²⁰⁷ pair is important for activation of the H₁-receptor by histamine. In contrast, analogues of 2-PhHist seem to belong to a distinct subclass of histamine agonists and an alternative mode of binding is proposed in which the 2-phenyl ring binds to the same receptor location as one of the aromatic rings of classical histamine H₁-antagonists. Subsequently, the binding modes of the agonists Hist, 2-MeHist and 2-PhHist and the H₁-antagonist cyproheptadine were evaluated in three different seven--helical models of the H₁-receptor built in homology with bacteriorhodopsin, but using three different alignments. Our findings suggest that the position of the carboxylate group of Asp¹¹⁶ (TM3) within the receptor pocket depends on whether an agonist or an antagonist binds to the protein; a conformational change of this aspartate residue upon agonist binding is expected to play an essential role in receptor stimulation.Abbreviations 2-MeHist 2-methylhistamine - 2-PEA 2-pyridyl-ethylamine - 2-PhHist 2-phenylhistamine - CHO Chinese hamster ovary - E_int interaction energy - E_str strain energy - GES global energy structure - gpH₁R guinea pig H₁-receptor - GPCR G-protein coupled receptor - Hist histamine - N proximal nitrogen - N tele nitrogen - TM transmembrane domain - WT wild type     

Hydrogen bonding-mediated foldamer-bridged zinc porphyrin-C60 dyads: ideal face-to-face orientation and tunable donor-acceptor interacion

Four porphyrin-bridge-C₆₀ dyads have been synthesized by covalently linking the chromophores at the opposite ends of a hydrogen bonded arylamide-derived foldamer bridge. For comparison, four C₆₀-free porphyrin derivatives of the same frameworks have also been prepared. The fully hydrogen bonded bridges enable the appended porphyrin and C₆₀ moieties to contact in a face-to-face manner. ¹H NMR, UV-vis and fluorescent investigations in chloroform indicate that such a structural matching remarkably facilitates the intramolecular energy and electron transfer and charge separation between the two chromophores and also retards the recombination of the charge-separated state. Removing one hydrogen bond considerably reduces the energy and electron transfer. Further removing another one leads to no important interaction between the chromophores to occur.     

Theoretical study on the (O2-HF) complex

The potential energy surface of the (O₂-HF)⁺ complex has been investigated theoretically. Equilibrium structure has been calculated at the UCCSD/6-311++G(2d,2p) and UCCSD/aug-cc-pVTZ levels of theory. Two stable complexes, T-shape and collinear, have been found on the surface whose interaction energies are calculated to be −12.36 and −10.19 kcal mol⁻¹, respectively, at the UCCSD(T)/aug-cc-pVTZ level after correcting for the basis set superposition error (BSSE). Natural bond orbital (NBO) analysis revealed intermolecular charge transfers occur followed by intramolecular charge rearrangement. A large contribution from the n_F to π* _OO is found.     

Molecular mechanics on bonding and non-bonding interactions in (atom@C60)

The interactions between the embedded atom X (X = Li, Na, K, Rb, Cs; F, Cl, Br, I) andC60 cage in the endohedral-form complexes (X@C₆₀) are calculated and discussed according to molecular mechanics from the point of view of the bonding and non-bonding. It is found from the computational results that for atoms with radii larger than Li’s, their locations with the minimum interaction in (X@C₆₀) are at the cage center, while atom Li has an off-center location with the minimum interaction deviation of ~0.05 nm, and the cage-environment in C₆₀ can be regarded as syhero-symmetry in the region with radiusr of ~0.2 nm. It is shown that the interaction between X and C₆₀ cage is of non-bonding characteristic, and this non-bonding interaction is not purely electrostatic. The repulsion and dispersion in non-bonding interactions should not be neglected, which make important contribution to the location with minimum interaction of X, at center or off center. Some rules about the variations of interactions with atomic radii have been obtained. Project supportt:d by the National Natural Science Foundation of China.