Effect Of Intramolecular Interactions Research Articles

Electrostatic Trapping of N_{2} Molecules in High Rydberg States.

N_{2} molecules traveling in pulsed supersonic beams have been excited from their X ^{1}Σ_{g}^{+} ground electronic state to long-lived Rydberg states with principal quantum numbers between 39 and 48 using a resonance-enhanced two-color three-photon excitation scheme. The Rydberg states populated had static electric dipole moments exceeding 5000 D which allowed deceleration of the molecules to rest in the laboratory-fixed frame of reference and three-dimensional trapping using inhomogeneous electric fields. The trapped molecules were confined for up to 10ms, with effective trap decay time constants increasing with principal quantum number, and ranging from 450 to 700 μs. These observations, and comparison with the results of similar measurements with He atoms, indicate that the decay dynamics of the trapped Rydberg N_{2} molecules are dominated by spontaneous emission and do not exhibit significant contributions from effects of intramolecular interactions that lead to non-radiative decay.

Newly designed Mn (III)–W(V) bimetallic assembly built by manganese (III) Schiff–base and octacyanotungstate(V) building blocks: Structural topologies, and magnetic features

New complex [Mn (SB)2(DMF)2] [W (CN)8] hereafter referred to as complex 1, which was prepared by self–assembly of [Mn (SB)2(DMF)2]3+ and [W (CN)8]3− and structurally characterized by elemental analysis, infrared (IR) and single crystal X–ray techniques (H2SB is Schiff base derived from the condensation of salicylaldehyde and N,N–diethylethylenediamine and DMF is dimethylformamide). The structure consists of 1–D supramolecular chains and further stacks to give a 3–D supramolecular architecture whose molecular fragments are linked by hydrogen bond as well as C − H···π interactions between [Mn (SB)2(DMF)2]3+ and [W (CN)8]3−. An underlying net for the representation consists of two types of fragments with 1,4 M5–1 and 1,8 M9–1 topologies and further illustration of the molecular network in terms of a graph−theory approach using simplification procedure resulted in the underlying net of 2C1topological type in the complex 1. Magnetic susceptibility measurements of complex 1 was carried out in the temperature range 2–300 K, indicates the presence of either magnetic anisotropy zero field splitting, the effect of intramolecular interactions, or both. Complex 1 follows the Curie–Weiss law with Curie constant value of 3.43 cm3mol−1K, and the slight negative Weiss constant (−0.60 K) value indicates the predominant antiferromagnetic magnetic exchange interactions.The magnetic properties of Title complex was investigated thoroughly and showed that ferromagnetic interaction between W(V) and Mn (III) operate via the intramolecular H–bonding interaction between cyanide nitrogens and a hydrogen atom.

Acid monomer analysis in waterborne polymer systems by targeted labeling of carboxylic acid functionality, followed by pyrolysis – gas chromatography

Pyrolysis – gas chromatography – (PyGC) is a common method to analyse the composition of natural and synthetic resins. The analysis of acid functionality in, for example, waterborne polyacrylates and polyurethanes polymers has proven to be difficult due to solubility issues, inter- and intramolecular interaction effects, lack of detectability in chromatographic analysis, and lack of thermal stability. Conventional analytical techniques, such as PyGC, cannot be used for the direct detection and identification of acidic monomers, due to thermal rearrangements that take place during pyrolysis. To circumvent this, the carboxylic acid groups are protected prior to thermal treatment by reaction with 2-bromoacetophenone. Reaction conditions are investigated and optimised wrt. conversion measurements. The aproach is applied to waterborne polyacryalates and the results are discussed. This approach enables identification and (semi)quantitative analysis of different acid functionalities in waterborne polymers by PyGC.

DFT studies on the favored and rare tautomers of neutral and redox cytosine

The complete tautomeric mixture consisting of nine prototropic tautomers has been studied in the gas phase at the DFT(B3LYP)/6-311+G(d,p) level for neutral, oxidized, and reduced cytosine. Rotational isomerism of the exo –OH group and geometrical isomerism of the exo =NH group have also been considered. Tautomeric conversions possible for cytosine have been compared with those for its structural models, 4-amino- and 2-hydroxypyrimidine. Effects of intramolecular interactions between neighboring groups for cytosine are analogous to those observed for model compounds. Although they are not very strong, they are sufficient to influence tautomeric equilibria and relative stabilities of individual tautomers. One-electron oxidation and one-electron reduction change tautomeric preferences. Tautomers that are rare forms for neutral cytosine become favored ones for oxidized and reduced cytosine. Aromaticity is not the main factor that dictates the tautomeric preferences. Stability of functional groups seems to be more important than full electron delocalization.

Conserved Modular Domains Team up to Latch-open Active Protein Kinase Cα

Signaling proteins comprised of modular domains have evolved along with multicellularity as a method to facilitate increasing intracellular bandwidth. The effects of intramolecular interactions between modular domains within the context of native proteins have been largely unexplored. Here we examine intra- and intermolecular interactions in the multidomain signaling protein, protein kinase Cα (PKCα). We identify three interactions between two activated PKC molecules that synergistically stabilize a nanomolar affinity homodimer. Disruption of the homodimer results in a loss of PKC-mediated ERK1/2 phosphorylation, whereas disruption of the auto-inhibited state promotes the homodimer and prolongs PKC membrane localization. These observations support a novel regulatory mechanism wherein homodimerization dictates the equilibrium between the auto-inhibited and active states of PKC by sequestering auto-inhibitory interactions. Our findings underscore the physiological importance of context-dependent modular domain interactions in cell signaling.

Molecular fragment shape variation index applied to intramolecular interaction studies

The fragment shape variation index approach is applied to intramolecular interactions involving C6 aromatic molecular fragments in the special case where the shape-modifying interactions are also caused primarily by other C6 aromatic fragments of the same molecule. This report is a part of a series of studies aimed at the detailed modeling of various components of intramolecular interactions among molecular fragments, including aromatic ring interactions, aromatic ring and non-aromatic conjugated and non-conjugated system interactions, and more general through-space and through-bond interactions. The ultimate purpose of these studies is a better understanding of the electron density shape modifying effects of intramolecular interactions.

Effect of intramolecular interaction on time growth of second moment of multiple quantum NMR in solids

The time dependence of the NMR multiple quantum spectrum in solids containing methyl groups is investigated. We studied both of types of the nuclear spin systems: namely linking by secular part of the mutual dipole-dipole interaction and linking by effective double quantum Hamiltonian. It is revealed for the first type of systems the rate with the time of the growing up of the second moment when intramolecular interaction is present becomes less in compare with situation when a strong intramolecular interaction is absent. On the contrary for the second type of Hamiltonian the above rate increases.

Structural, vibrational and hyperpolarizability calculation of ( E)-2-(2-hydroxybenzylideneamino)-3-methylbutanoic acid

The ( E)-2-(2-hydroxybenzylideneamino)-3-methylbutanoic acid ( E)-2HBAMBA was synthesized. The FT-IR, FT-Raman and UV–vis spectra have been recorded and characterized. Theoretical wavenumbers along with IR and Raman intensities were calculated using B3LYP/6-31G(d,p) level and total energy distribution (TED) of the various normal mode of vibrations were also studied. The conformational analysis was performed for a stable conformer by selecting the dihedral angles and the optimized bond parameters were calculated for the stable structure. Effect of intramolecular interactions is calculated by changing the orientation of hydroxyl hydrogen. To know the charge transfer while changing the hydroxyl group hydrogen orientation, the NBO analysis was performed. Using the same level of calculation, the electronic charge transfers were calculated and compared.

The Intramolecular Impact to the Sequence Specificity of B→A Transition: Low Energy Conformational Variations in AA/TT and GG/CC Steps

It is well known, that local B→A transformation in DNA is involved in several biological processes. In vitro B↔A transition is sequence-specific. The physical basis of this specificity is not known yet. Here we analyze the effect of intramolecular interactions on the structural behavior of the GG/CC and AA/TT steps. These steps exemplify sequence specific bias to the B- or A-form structure. Optimization of potential energy of the molecular systems composed of an octanucle-otide, neutralized by Na+ and solvated with TIP3P water molecules in rectangular box with periodic boundary conditions gives the statistically representative sets of low energy structures for GG/CC and AA/TT steps in the middle of the diverse flanking sequences. Permissible 3D variations of GG/CC and AA/TT, and correlation of the relative motion of base pairs in these steps were analyzed. AA/TT step permits high variability for low energy conformers in the B-form DNA and small variability for low energy conformers in the A-form DNA. In contrast GG/CC step permits high variability for low energy conformers in the A-form DNA and small variability for low energy conformers in the B-form DNA. The relative motion of base pairs in GG/CC step is high correlated, while in AA/TT step this correlation is notably less. Atom-atom interactions inside-the-step always favors the B-form and their component - stacking interactions (atomatom interactions between nucleic bases) is crucial for the duplex stabilization. Formation of the A-form for both steps is a result of interactions with the flanking sequences and water-cation environment in the box. The average energy difference between conformations presenting B-form and A-form for the GG/CC step is high, while for the AA/TT step it is rather low. Thus, intramolecular interactions in GG/CC and AA/TT steps affect the possible conformational diversity (“conformational entropy”) of the A- and B- type structures of DNA step. This determines the known bias of the A-form DNA depending on the enrichment of sequences with GG/CC. If structural tuning during the process of protein-DNA complex formation lead to the local B→A transformation of DNA, it is largely directed by high conformational diversity of GG/CC step in the A-form. In such a case the presence in the target site of both kinds of examined steps ensures the reversible character of ligand binding.

The role of ring substituents on hydrogen bonding of 5-cyano-2-hydroxyacetophenone and 2-hydroxy-4-methoxy-5-nitroacetophenone in the ground and excited states

The crystal structures of two ortho-hydroxyacetophenones (5-cyano-2-hydroxyacetophenone and 2-hydroxy-4-methoxy-5-nitroacetophenone) were determined by X-ray diffraction at 100 K. These experimental values are compared with quantum mechanical DFT calculations (B3LYP/6-311++G(d,p)). DFT calculations have resulted in potential energy surfaces for the ground state (GSPES). The effect of intramolecular interactions, in particular of intramolecular hydrogen bonds, on steady-state fluorescence spectra in non-polar solvents and solid state at room temperature show interesting results. Excited state intramolecular proton transfer (ESIPT) was evidenced by a large Stokes shifted fluorescence (∼11,000 cm −1). Intensive fluorescence was observed in the solid state of 5-cyano-2-hydroxyacetophenone.

Effect of intramolecular interactions on circular dichroism of ortho-substituted 1-phenethylamines.

The synthesis of ortho-substituted (S)-1-phenethylamines via ortho-lithiation of its N,N-dimethyl derivative followed by reactions with different reagents is described. Circular dichroism spectra of synthesized compounds were measured. It is shown that the observed short-wave Cotton effects greatly depend on the existence of cyclic structure due to possible interactions such as hydrogen bond or electrostatic interaction.

Effect of intramolecular interaction between polar and polarizable bonds on13C shielding constants in different conformations of 2-methoxy- and 2-vinyloxynaphthalene molecules: Anab initio study

Shielding constants of13C nuclei calculated for different conformations of 2-methoxynaphthalene and 2-vinyloxynaphthalene molecules by the GIAOab initio method in the D95** basis set indicate a strong shielding effect of the intramolecular interaction between the polar O−C bond of the substituent and the polarizable π-bond of the naphthyl moiety on the C atom incis-position. The results obtained are in agreement with the experimentally found trends of changes in the chemical shifts of13C nuclei and are in reasonable quantitative agreement with experimental data.

Excess Enthalpies of Binary Mixtures of 2-Propen-1-Ol with Chloroalkanes and Chloroalkenes at 298.15 K

Abstract Excess molar enthalpies of binary mixtures of 2-propen-1-ol with 1,2-dichloroethane, 1,1,1,-trichloroethane, 1,1,2,2-tetrachloroethane, trichloroethylene and tetrachloroethylene have been measured at 298.15 K using a 1451 Parr model solution calorimeter. The excess enthalpy values are positive in all the systems over the entire range of mole fraction except for the system involving 1,1,2,2-tetrachloroethane. All the excess enthalpy curves are found to be S shaped. Comments on the effect of intramolecular interactions on the intermolecular interactions have been made on the basis of the experimental results.

Effect of intramolecular interactions on the miscibility windows of PVC blends with modified SAN copolymers

AbstractWe investigated the miscibility windows in the blends of poly(vinyl chloride) (PVC) with chemically modified styrene/acrylonitrile (SAN) copolymers such as α‐methyl styrene/acrylonitrile (α SAN), α‐methyl styrene/methacrylonitrile (MSMAN). The blends of PVC with α SAN were found to have the broader miscibility window. This enhanced miscibility was interpreted in terms of intramolecular repulsion that originates from unfavorable interaction between counits of the copolymers and also intramolecular association of AN units. The intramolecular interactions were studied by using Fourier transform infrared (FT‐IR) spectroscopy. These interactions were reflected by a peak broadening in the nitrile stretching band in the acrylonitrile segments. The intermolecular interactions governing the miscibility in the blends of PVC with the series of copolymers were also discussed.

Effect of intramolecular interactions on the intensity of IR bands of identical bonds under conditions close to resonance

Effect of intramolecular interactions on the intensity of IR bands of identical bonds under conditions close to resonance

Hydration Thermodynamics of Biomolecules. IV. Hydration Free Energy of Amino Acid Related Molecules

Analysis of the free energy of transfer from gas phase to water has been made on forty organic molecules carrying the same atomic group as natural amino acids, where their conformation distribution and the effect of intramolecular interactions are explicitly considered. The best model is presented for classifying all the constituent atoms into hydration-thermodynamically different groups. The atomic hydration parameter, i.e. the transfer free energy per unit accessible surface area, is determined for each group. The intrinsic hydration energies of sulfur, oxygen and nitrogen atoms are estimated. Applicability to polar atoms of the assumption that the hydration free energy of a molecule can be given by a linear combination of accessible surface areas of the constituent atoms, is examined. The transfer free energy of an amino acid is shown to be significantly affected by the spatial interference between its main chain and side chain atoms.

Excess enthalpies of binary mixtures of acetophenone with benzene and substituted benzenes

Excess molar enthalpies of binary mixtures of acetophenone with benzene, toluene, o-xylene, m-xylene, p-xylene, chlorobenzene, bromobenzene and nitrobenzene have been measured at 298.15 K over the entire range of composition with a solution calorimeter. The excess enthalpies are positive in all the systems over the entire mole fraction range. Comments on the effect of intramolecular interactions on intermolecular interactions are made on the basis of the results.

Model calculations of chemical interactions. Part 1.—Intramolecular interactions and rotational barriers

A new procedure is introduced for the analysis of the effects of intramolecular interactions. Based on the most intuitive chemical picture of the energy differences between conformers, the procedure leads to explanations in terms of interactions between chemically meaningful subsystems into which the molecule can be conceptually partitioned, yet avoiding the concepts of antibond orbitals and bond–antibond interactions of the BO model. Use is made of the ab initio approximation with a minimal basis set of symmetrically orthogonalized hybrid AOs. Ethane, methylamine, methanol, propene, butadiene, glyoxal, hydrazine and hydroxylamine have been chosen as test molecules for the study of internal rotation.

Absorption of benzene derivatives through the body surface and gill membranes of goldfish: substitutent and intramolecular interaction effects

The substituent effects on the absorption rate constants ( k fish) of 35 benzene derivatives at pH 6.0 through the body surface and gill membranes of the goldfish were examined in terms of the substituent constant ( K s) and the intramolecular interaction constant ( K I), and the substituent effects were compared with those reported for the rat intestinal absorption rate constants ( k rat) at pH 6.0. The substituent groups giving positive or negative K s values were the same for the two goldfish membranes and the rat intestine. All the K I values were positive for the two goldfish membranes as well as for the rat intestine. The logarithmic values of k rat showed good correlations with those of k fish in both body surface ( r = 0.870, n = 34) and gills ( r = 0.860, n = 35). However, the k fish values of salicylic acid, p-hydroxybenzamide, and phenol in the body surface and those of the former two in the gills were significantly outside the critical region ( P < 0.05). The effects of substituent groups (increase or decrease) and intramolecular interaction (increase) on the k fish values were qualitatively the same as those on the k rat values and quantitatively correlated well with those on the k rat values, except in the cases of salicylic acid, phenol, and p-hydroxybenzamide. It was concluded that the substituent effects on the k fish values can be explained in terms of K S and K I, as in the case of rat intestine, but the effects on the k fish values of salicylic acid, phenol, and p-hydroxybenzamide can not.

Effect of intramolecular interactions on the complexing capacity of p-XC6H4OR Ethers

The complexing capacity in p-XC6H4OR ethers relative to tetracyanoethylene as a π-acceptor is determined by the reverse and direct polar conjugation between the X and OR substituents.