Hydrogen bonding in different pyrimidine–methanol clusters probed by polarized Raman spectroscopy and DFT calculations

We report on the hydrogen bonding between pyrimidine (Pd) and methanol (M) as H‐donor in this study. Hydrogen bonds between pyrimidine and methanol molecules as well as those between different methanol molecules significantly influence the spectral features at high dilution. The ring‐breathing mode ν₁ of the reference system Pd was chosen as a marker band to probe the degree of hydrogen bonding. Polarized Raman spectra in the region 970–1020 cm⁻¹ for binary mixtures of (pyrimidine + methanol) at 28 different mole fractions were recorded. A Raman line shape analysis of the isotropic Raman line profiles at all concentrations revealed three distinct spectral components at mole fractions of Pd below 0.75. The three components are attributed to three distinct groups of species: ‘free Pd’ (pd), ‘Pd with low methanol content’ (pd1) and ‘Pd with high‐methanol content’ (pd2). The two latter species differ considerably in the pattern and the strengths of the hydrogen bonds. The results of density functional theory calculations on structures and vibrational spectra of neat Pd and eight Pd/M complexes with varying methanol content support our interpretations of the experimental results. A nice spectra–structure correlation for the different cluster subgroups was obtained, similar to earlier results obtained for Pd and water. Apart from N···H and O···H hydrogen bonds between pyrimidine and methanol, O···H hydrogen bonds formed among the methanol molecules in the cluster at high methanol content also play a crucial role in the interpretation of the experimental results. Copyright © 2010 John Wiley & Sons, Ltd.     

Theoretical study of cooperativity between hydrogen bond‒hydrogen bond,halogen bond‒halogen bond and hydrogen bond‒halogen bond in ternary FX…diazine…XF (X = H and Cl) complexes

ABSTRACT

In the present work, the cooperativity between hydrogen bond?hydrogen bond, halogen bond?halogen bond and hydrogen bond?halogen bond in ternary FX…diazine…XF (X = H and Cl) complexes is theoretically investigated. The sign of cooperative energy (E_coop) obtained in all of the triads is positive which indicates that the ternary complex is less stable than the sum of the two isolated binary complexes. Moreover, our calculations show that E_coop value in triads increases as FX…pyridazine…XF > FX…pyrimidine…XF > FX…pyrazine…XF. In agreement with energetic, geometrical and topological properties, electrostatic potentials and coupling constants across ¹⁵N…X?¹⁹F (X = ¹H or ³⁵Cl) hydrogen and halogen bonds indicate that hydrogen and halogen bonds are weakened in the considered complexes where two hydrogen and halogen bonds coexist. As compared to N…H hydrogen bond, it is also observed that cooperativity has greater effect on N…Cl halogen bond.     

Ramsey terms for two-, three-, and four-bond coupling involving 15N and 17O in hydrogen-bonded and nonhydrogen-bonded systems: are coupling constants sensitive to RAHBs?

Ab initio EOM-CCSD/(qzp,qz2p) calculations have been performed on complexes with intermolecular hydrogen bonds involving ¹⁵N and ¹⁷O, and molecules with and without intramolecular hydrogen bonds involving these nuclei. Coupling constants across intermolecular hydrogen bonds are well approximated by the Fermi-contact (FC) term. In general, ^2hJ(X–Y) for intramolecular coupling across X–H^…Y hydrogen bonds are not sensitive to the presence of resonance-assisted hydrogen bonds (RAHBs). However, ^2hJ(O–O) for coupling across the intramolecular hydrogen bond in malonaldehyde is greater than ^2hJ(O–O) for its saturated counterpart, so that ^2hJ(O–O) is sensitive to the presence of the RAHB. This is also the case for the sulphur analogues of malonaldehyde. For these unsaturated hydrogen-bonded molecules, molecules with carboxyl groups, and trans-glyoxal, J is dominated by the paramagnetic spin orbit (PSO) term. For these systems, the primary mode of coupling transmission is through the conjugated chain. For complexes with intermolecular hydrogen bonds, saturated molecules with intramolecular hydrogen bonds, unsaturated and saturated molecules in which the hydrogen bond has been broken, and unsaturated molecules with intramolecular N–H^…N or O–H^…N hydrogen bonds, J is dominated by the FC term. FC domination in hydrogen-bonded systems indicates that the primary transmission mode is across the hydrogen bond.     

Piezoelectric properties of non-uniform polymeric structures under static load

ABSTRACT

Piezo-electrical properties of structures containing ‘soft’ and ‘hard’ dielectric layers with charge stored on the interfaces are described in the paper. The piezo-activation process of structures containing layers with gas voids by partial discharges is described. The influence of the mechanical properties of the ‘soft’ layer on the piezoelectric parameter d₃₃ value and its dependence on the static pressure p are also discussed. It was found experimentally, that for the fibrous type of ‘soft’ dielectric layer, the dependence of the piezoelectric parameter d₃₃ (p) can be described by the function d₃₃ ÷ p^?n, where n ≤ 1.     

Pnicogen bonds in complexes with CO and CS: differentiating properties

ABSTRACT

Ab initio MP2/aug’-cc-pVTZ calculations have been performed on pnicogen-bonded complexes with CO and CS as electron-pair donors to PH₂X, for X?=?F, NC, OH, CN, CCH, and H. CO:PH₂X and OC:PH₂X complexes are stabilised by traditional pnicogen bonds. CS is an electron-pair donor through its in-plane π system to four PH₂X molecules. It forms C···^?P phosphorus-shared bonds with some ion-pair character with PH₂F, PH₂(OH-Z), and PH₂(OH-E), and traditional pnicogen bonds with all PH₂X except PH₂F. C-O and C-S stretching frequencies are blue-shifted for C···P pnicogen bonds, and red-shifted for O···P and S···P bonds. EOM-CCSD spin-spin coupling constants ^1pJ(P-C) for OC:PH₂X and ^1pJ(P-O) for CO:PH₂X are characteristic of complexes stabilised by traditional pnicogen bonds. Coupling constants ^1pJ(P-C) as a function of the P-C distance for SC:PH₂X illustrate the evolution of the C···P pnicogen bond. They increase as the P-C distance decreases in complexes with traditional bonds, reach a maximum for SC:PH₂OH transition structures as the P-C distance further decreases and the bonds gain phosphorus-shared character, and then change sign and continue to decrease as the P-C distance further decreases and the phosphorus-shared pnicogen bonds gain ion-pair character. They approach the values of ¹J(P-C) for the cation (H₂PCS)⁺.     

Quantum-Chemical Investigation of the Intermolecular Interaction Effect on the Spectral-Luminescent and Physical-Chemical Properties of Certain 8-Azasteroid Class Molecules

The effect of hydrogen bonds on the spectral-luminescent and proton-acceptor properties of 8-azagone-12,17-dione and its 2,3-dimethoxy substituent is examined. The method of molecular electrostatic potential is used for choosing a spatial model for complexes with the 1:2 mixture ratio. Hydrogen bonding of oxygen atoms of C and D cycles of both molecules with water molecules is shown to affect but slightly the spectral-luminescent properties. The effect of hydrogen bonds on the proton-acceptor properties of molecules both in the ground and fluorescent states is most pronounced: the proton-acceptor properties of oxygen atoms of the C, D, and methoxy groups decrease, particularly in the fluorescent state, while the same properties of the nitrogen atom increase. We can assume on the basis of these facts that the role of the nitrogen atom in the intermolecular interaction is increased when it is in the S ₁ state.     

Weak interactions and cooperativity effects on disiloxane: a look at the building block of silicones

The behaviour of disiloxane 1 towards a set of Lewis acids (LA) and Lewis bases (LB) forming complexes through its oxygen and silicon atoms, respectively, was studied at the MP2/aug′-cc-pVTZ level of theory, exploring a wide variety of non-covalent interactions. Disiloxane is a moderate electron acceptor and a good electron donor, exhibiting in the latter case binding energies up to almost ?100 kJ/mol with BeCl₂. Cooperativity effects were also analysed by looking at ternary 1:LA:LB complexes. Shorter intermolecular distances than in the corresponding binary complexes and a negative contribution of the three-body term to the binding energy indicate that the non-covalent interactions allowed by disiloxane through its acid and basic centres cooperate between them to reinforce both donor–acceptor pairs. These effects are particularly strong in complexes involving beryllium and triel bonds, but are also relevant for complexes containing hydrogen bonds.     

Symmetric bifurcated halogen bonds: substituent and cooperative effects

ABSTRACT

The aim of this study is to investigate the geometries, interaction energies and bonding properties of the symmetrical bifurcated halogen bond interactions (BXBs) by means of ab initio calculations. For this purpose, the NCX (X = Cl, Br) molecule is paired with a series of N-formyl formamide (NFF) derivatives (NFF-Z, Z = H, CN, CCH, OH, CH₃ and Li), and the properties of the resulting complexes are studied by molecular electrostatic potential, quantum theory of atoms in molecules, noncovalent interaction index and natural bond orbital analyses. For a fixed NCX molecule, interaction energies increase in the order of Z = Li > CH₃ > H > OH > CCH > CN. We found a strong correlation between the interaction energies of NCX:NFF-Z complexes and molecular electrostatic potential minimum values associated with NFF-Z monomers. Moreover, cooperative effects between BXB and X???N halogen bond interactions are studied in the ternary NCX:NCX:NFF-Z systems. Our results indicate that the strength of BXB interactions in the ternary complexes is enhanced by the presence of X???N bonds. Besides, cooperativity effects tend to increase the covalency of BXBs in these systems.     

Cluster-solid interactions: A molecular dynamics investigation

Abstract

The interaction of small energetic clusters of metal atoms with surfaces has been investigated by molecular dynamics computer simulations. A wide variety of cluster-solid combinations have been studied so that the effects of the energy, size, and angle of incidence of the cluster, and the relative elastic properties of the cluster and substrate could be elucidated. ‘Soft landings’ were also investigated. From these studies, a mechanism map for cluster-solid interactions is developed. The results have particular importance for cluster beam deposition of thin films. The simulations are fully dynamical and 3-dimensional; they employ embedded-atom method potentials, which have been modified for interactions at close separations. A scheme for reducing the CPU time that is required for these and other simulations of radiation effects is described.     

Technical Reports: Atoms to Aerosols—The Chemical Dynamics Beamline

Chemical dynamics is the study of the elementary processes and interactions in chemistry. Fundamental properties such as dipole moments, ionization energies, electron affinities, proton affinities, and electronic structure all contribute to the photochemistry, radiationless processes and reactivity underlying all physical processes. The making and breaking of chemical bonds, and the energy partitioning in chemical systems after transformation, are also in the domain of chemical dynamics.

The valence shell, the outermost shell of electrons in a system, contributes most to the physical properties of material. It is these electrons that are shared in covalent bonding, transferred in ionic systems, coupled to form bands in bulk material, and interact most strongly with the environment.     

DFT-based study of the impact of transition metal coordination on the charge transport and nonlinear optical (NLO) properties of 2-{[5-(4-nitrophenyl)-1,3,4-thiadiazol-2-ylimino]methyl}phenol

Theoretical investigations of the impact of transition metal chelation on the electron/hole-transport and nonlinear optical (NLO) properties of 2-{[5-(4-nitrophenyl)-1,3,4-thiadiazol-2-ylimino]methyl}phenol (L) are reported herein. Calculations were carried out via density functional theory (DFT)-based methods, employing exchange–correlation functionals and basis sets of different qualities. Results have shown that free L is a moderate electron/hole-transporter, but that its Pd(II) and Pt(II) complexes are excellent hole- and electron-transport materials respectively, owing to their very small reorganisation energies and relatively large electronic coupling matrix elements or transfer integrals. These results indicate that the complexes are potentially suitable charge transport materials for the construction of organic light emitting diodes (OLEDs). Nevertheless, the results also revealed a higher NLO activity for L than its metal complexes. Interestingly, the first and second hyperpolarizabilities, along with some computed NLO properties of both L and its complexes are found to be remarkably higher than those of the prototypical push–pull molecule, para-nitroaniline. Accordingly, these compounds are potential candidates for the fabrication of optoelectronic and photonic devices for second- and third-order NLO applications. Summarily, metal chelation is found to enhance the charge transport properties in some cases, and to slightly diminish NLO response of L in all cases investigated.     

New phenomena in the propagation of optical waves through random media

Abstract

A review is presented of some new and exciting phenomena regarding the multiple scattering of optical waves in random systems. In particular, the author develops the important role played by the vector nature of the wave on memory effects (the ‘polarization memory effect’), correlations and statistical fluctuations (‘microstatistics’). He also describes the recent progress on the effect of a restricted geometry on correlation phenomena and nonRayleigh statistics.     

Synthesis, Characterization and DNA-binding Properties of Ln(III) Complexes with 6-Ethoxy Chromone-3-Carbaldehyde Benzoyl Hydrazone

A novel 6-ethoxy chromone-3-carbaldehyde benzoyl hydrazone (L) and its Ln(III) complexes, [Ln = Sm (1), Eu (2), Gd (3), Tb (4)], have been synthesized and characterized. The fluorescence properties of the Eu(III) and Sm(III) complexes in solid state and Eu(III) complex in different solutions (DMF, DMSO, methanol and acetonitrile) were investigated. At the same time, the DNA-binding properties of the two complexes are investigated using UV-Vis absorption spectroscopy, fluorescence spectroscopy, viscosity measurement. All the experimental evidences indicate that the two complexes can bind to CT-DNA via an intercalation mechanism. Furthermore, antioxidant activity tests in vitro showed that the complexes have significant antioxidative activity against hydroxyl free radicals from the Fenton reaction.     

Search for singlet-triplet bistability or biradicaloid properties in polycyclic conjugated hydrocarbons: a valence-bond analysis

Two classes of molecules displaying singlet-triplet biradical bistability (i.e. species having significant biradicaloid properties) can be designed as follows. Alternant conjugated polycyclic hydrocarbons with numerous fixed double bonds (double bonds that remain unchanged in all its Kekulé resonance structures), a large number of Dewar resonance structures which measures the corresponding diradical resonance, and a small HOMO-LUMO band gap which measures the ease of thermal spin inversion are candidates for singlet triplet biradical bistability. Chichibabin's hydrocarbon ( 1 ) is an example. In addition, in the search for candidate molecules having singlet triplet bistability, one should also examine polycyclic conjugated systems having nonalternant induced spin frustration. Spin frustrated nonalternant polycyclic conjugated hydrocarbons will display singlet-triplet bistability (biradicaloid properties) and are generated from alternant valence-bond diradicals or Hückel molecular orbital diradicals having classical Kekulé structures by appropriate intramolecular joining of two starred or nonstarred positions with bonds, respectively.     

DFT/TDDFT investigation on the photophysical properties of a series of phosphorescent cyclometalated complexes based on the benchmark complex FIrpic

The photophysical properties of four Ir(III) complexes have been investigated by means of the density functional theory/time-dependent density functional theory (DFT/TDDFT). The effect of the electron-withdrawing and electron-donating substituents on charge injection, transport, absorption and phosphorescent properties has been studied. The theoretical calculation shows that the lowest-lying singlet absorptions for complexes 1–4 are located at 387, 385, 418 and 386 nm, respectively. For 1–4, the phosphorescence at 465, 485, 494 and 478 nm is mainly attributed to the LUMO → HOMO and LUMO → HOMO-1 transition configurations characteristics. In addition, ionisation potential (IP), electron affinities (EAs) and reorganisation energy have been investigated to evaluate the charge transfer and balance properties between hole and electron. The balance of the reorganisation energies for complex 3 is better than others. The difference between hole transport and electron transport for complex 3 is the smallest among these complexes, which is beneficial to achieve the hole and electron transfer balance in emitting layer.     

Tuning of carbon bonds by substituent effects: an ab initio study

ABSTRACT

An ab initio study, at the MP2/aug-cc-pVTZ level of theory, is performed to study σ-hole bond in binary XH₃C···CNY complexes, where X = CN, F, NO₂, CCH and Y = H, OH, NH₂, CH₃, C₂H₅, Li. This type of interaction is labelled as ‘carbon bond’, since a covalently bonded carbon atom acts as the Lewis acid in these systems. The geometrical and energetic parameters of the resulting complexes are analysed in details. The interaction energies of these complexes are between ?4.97 kJ/mol in (HCC)H₃C···CNH and ?23.07 kJ/mol in (O₂N)H₃C···CNLi. It is found that the electrostatic interaction plays a key role in the overall stabilisation of these carbon-bonded complexes. To deepen the understanding of the nature of the carbon-bonding, the molecular electrostatic potential, natural bond orbital, quantum theory of atoms in molecules and non-covalent interaction index analyses are also used. Our results indicate that the carbon bond is favoured over the C-H···C hydrogen bond in the all complexes considered and may suggest the possible important roles of the C···C interactions in the crystal growth and design.     

Molecular dynamics study of hydrogenated silicon clusters at high temperatures

This paper reports on a study of the stability of silicon clusters of intermediate size at a high temperature. The temperature dependence of the physicochemical properties of 60- and 73-atom silicon nanoparticles are investigated using the molecular dynamics method. The 73-atom particles have a crystal structure, a random atomic packing, and a packing formed by inserting a 13-atom icosahedron into a 60-atom fullerene. They are surrounded by a ‘coat’ from 60 atoms of hydrogen. The nanoassembled particle at the presence of a hydrogen ‘coat’ has the most stable number (close to four) of Si–Si bonds per atom. The structure and kinetic properties of a hollow single-layer fullerene-structured Si₆₀ cluster are considered in the temperature range 10 K ≤ T ≤ 1760 K. Five series of calculations are conducted, with a simulation of several media inside and outside the Si₆₀ cluster, specifically, the vacuum and interior spaces filled with 30 and 60 hydrogen atoms with and without the exterior hydrogen environment of 60 atoms. Fullerene surrounded by a hydrogen ‘coat’ and containing 60 hydrogen atoms in the interior space has a higher stability. Such clusters have smaller self-diffusion coefficients at high temperatures. The fullerene stabilized with hydrogen is stable to the formation of linear atomic chains up to the temperatures 270–280 K.     

Helical ordering of hydrogen bonds between pairs of DNA bases

The interaction between hydrogen bonds and conformational elastic degrees of freedom has been investigated using the simplest model of a double-strand DNA molecule. The hydrogen bonds are described in terms of two-level quantum systems. After excluding conformational degrees of freedom, one has effective interaction among two-level systems. In the ground state of an ideal double helix, hydrogen bonds in a DNA molecule also have a helical order induced by conformational degrees of freedom. The pitch of the hydrogen-bond helix (and even its sign under certain conditions) is different from that of the basic helix pitch and, generally speaking, is incommensurate with the latter. This effect can, possibly, lead to an inversion of the sign of the circular dichroism in spectral bands, which was detected in some experiments. Zh. éksp. Teor. Fiz. 115, 940–950 (March 1999)     

An Assessment of the Assignment of Characteristic N-O Vibrations in Aromatic N-Oxides

The use of “characteristic” N-O group frequencies, in characterising metal complexes with aromatic N-oxides is widespread. The most popular assignments of the N-O in-plane and out-of-plane bends of N-oxides are shown to be in error, while the validity of transferring the N-O assignments of pyridine N-oxide to larger aromatic N-oxide systems is cautioned.     

Softening and hardening of yield stress by hydrogen–solute interactions

Abstract

Hydrogen atoms have a wide variety of effects on the mechanical performance of metals, and the underlying mechanisms associated with effects on plastic flow and embrittlement remain to be discovered or validated. Here, the reduction in the plastic flow stress (softening) due to hydrogen atoms in solute-strengthened metals, previously proposed by Sofronis et al. is demonstrated at the atomistic level. Glide of an edge dislocation through a field of solutes in a nickel matrix, both in the absence of hydrogen and in the presence of H bound to the solutes, is modelled. The ‘solutes’ here are represented by vacancies, enabling use of accurate binary Ni–H interatomic potentials. Since vacancies have a misfit strain tensor in the Ni matrix and also bind hydrogen atoms, they are excellent surrogates for study of the general phenomenon. The binding of H to the solute (vacancy) reduces the misfit volume to nearly zero but also creates a non-zero tetragonal distortion. Solute strengthening theory is used to establish the connection between strength and solute/hydrogen concentration and misfit strain tensor. Simulations show that when a dislocation moves through a field of random vacancy ‘solutes’, the glide stress is reduced (softening) when H is bound to the solutes. Trends in the simulations are consistent with theory predictions. Trends of softening or hardening by H in metal alloys can thus be made by computing the misfit strain tensor for a desired solute in the chosen matrix with and without bound hydrogen atoms. Pursuing this, density functional theory calculations of the interaction of H with carbon and sulphur solutes in a Ni matrix are presented. These solutes/impurities do not bind with H and the complexes have larger misfit strains, indicative of H-induced strengthening rather than softening for these cases. Nonetheless, H/solute interactions are the only mechanism, to date, that shows nanoscale evidence of plastic softening due to hydrogen associated with the hydrogen-enhanced localised plasticity concept in fcc metals.