Search results for "INTERACTION"

Kinetics of rat CSD-C2 binding to H3.3 RNA

2017

Cold-shock domain containing protein C2 (CSD-C2; also known as PIPPin) is an RNA-binding protein conserved in the evolution that interacts with the 3’-untranslated region (3’-UTR) of rat H1.0 and H3.3 histone messengers. Biolayer interferometry (BLI) is a technique that measures changes in an interference pattern generated from visible light, reflected from an optical layer, and a biolayer which contains molecules of interest. In this study, we used the BLI methodology in order to analyze and describe the binding properties of CSD-C2 and the mRNA encoding the rat brain histone protein H3.3. Recombinant CSD-C2 was incubated with in vitro transcribed, and biotinylated H3.3 RNA fragments bound…

An ab initio CI study on the rotational barrier of the allyl anion

1986

All-electron and pseudopotential non-empirical calculations have been performed on C 2v and C s (syn, anti) allyl anion conformations. Using a double-zeta valence-shell basis set within the Epstein-Nesbet definition of the unperturbed Hamiltonian, a value about 19 kcal/mol is found for the barrier to rotation of the allyl anion. This value is the theoretical value obtained with greater accuracy, and the lowest one for the rotational barrier.

Use of response factorial design for process optimization of basic dye adsorption onto activated carbon derived from Persea species

2017

Abstract Full factorial design is a powerful and efficient mathematical approach widely applied in the optimization of response. The important parameters which affect the removal efficiency of methylene blue such temperature, initial pH of the solution, concentration and adsorbent dosage were optimized. They coded as A, B, C and D, consecutively, and were investigated at two levels (+ 1 and − 1). A linear mathematical model representing the influence of the different variables and their interactions was obtained. Main effect, Normal probability plot of residuals, analysis of variance (ANOVA), surface plots, and contour plots were used to study the effects and interaction effects between ope…

ChemInform Abstract: Weak Interactions Between Trivalent Pnictogen Centers: Computational Analysis of Bonding in Dimers X3E···EX3(E: Pnictogen, X: Ha…

2009

The nature of weak interactions in dimers X3E···EX3 (E = N−Bi, X = F−I) was investigated by wave function and density functional theory (DFT)-based methods. Out of the 20 systems studied, 10 are found to be bound at the CP-MP2 and LMP2 levels of theory. Detailed partition of the interaction energy into different components revealed that dispersion is the primary force holding the dimers together but there also exists an important ionic component whose contribution increases with increasing halogen size. As expected, standard density functionals fail to describe bonding in the studied systems. However, the performance of DFT methods can be easily improved via empirical dispersion correction …

Analytic calculation of the diagonal Born-Oppenheimer correction within configuration-interaction and coupled-cluster theory

2006

Schemes for the analytic calculation of the diagonal Born-Oppenheimer correction (DBOC) are formulated and implemented for use with general single-reference configuration-interaction and coupled-cluster wave function models. Calculations are reported to demonstrate the convergence of the DBOC with respect to electron-correlation treatment and basis set as well as to investigate the size-consistency error in configuration-interaction calculations of the DBOC. The importance of electron-correlation contributions to the DBOC is illustrated in the computation of the corresponding corrections for the reaction energy and activation barrier of the F + H2 --FH + H reaction as well as of the atomiza…

A mutliconfigurational study of low-lying electronic states of KO

1992

Abstract Potential energy curves and spectroscopic parameters of several electronic states of the KO molecule have been calculated using multi-configurational methods. The KO B 2Π state, first time theoretically described, presents a strong avoided crossing with the A 2Π state, and allows for the explanation of the observed fluorescence of the KO molecule. Eleven electronic states have been studied at all the internuclear distances. Effects of complete active space and basis set selections on the results are also analyzed.

Phenylethynyl- and Phenylethenylmetacyclophanes with π,π Interactions

1999

Full configuration interaction calculation of BeH adiabatic states.

2008

An all-electron full configuration interaction (FCI) calculation of the adiabatic potential energy curves of some of the lower states of BeH molecule is presented. A moderately large ANO basis set of atomic natural orbitals (ANO) augmented with Rydberg functions has been used in order to describe the valence and Rydberg states and their interactions. The Rydberg set of ANOs has been placed on the Be at all bond distances. So, the basis set can be described as 4s3p2d1f3s2p1d(BeH)+4s4p2d(Be). The dipole moments of several states and transition dipole strengths from the ground state are also reported as a function of the R(Be-H) distance. The position and the number of states involved in sever…

Hydration of agarose double helix: A monte carlo simulation

2009

The structure of the water around agarose double helix is analyzed with ab initio quantum mechanical calculations and Monte Carlo simulations. The potential surface is sampled by computing the interaction energy between fragments of agarose and a water molecule placed at 221 different orientations and/or positions. These energy values are fitted to a simple analytical expression representing atom-atom pair potentials for a water molecule interacting with agarose. A preliminary understanding of the agarose-water interaction is obtained from isoenergy contour maps at planar cross sections, perpendicular to the long axis of the double helix, and for cylindrical surfaces enclosing the double he…

A study of coronene?coronene association using atom?atom pair potentials

1996

A study of the coronene—coronene association using different interaction potentials based on an atom-atom pair potential proposed by Fraga has been performed. The interaction potentials employed differ in the way the electrostatic and/or dispersion contributions are computed. The influence of both contributions on the geometries predicted for the coronene dimer is discussed in order to analyze the effectiveness of the different interaction potentials. The stationary points found in each interaction energy hypersurface are characterized by calculating the Hessian eigenvalues. Results are discussed in the light of those previously reported for the benzene dimer. Stacked-displaced structures a…