Minimum MD simulation length required to achieve reliable results in free energy perturbation calculations: Case study of relative binding free energies of fructose‐1,6‐bisphosphatase inhibitors

In an attempt to establish the criteria for the length of simulation to achieve the desired convergence of free energy calculations, two studies were carried out on chosen complexes of FBPase‐AMP mimics. Calculations were performed for varied length of simulations and for different starting configurations using both conventional‐ and QM/MM‐FEP methods. The results demonstrate that for small perturbations, 1248 ps simulation time could be regarded a reasonable yardstick to achieve convergence of the results. As the simulation time is extended, the errors associated with free energy calculations also gradually tapers off. Moreover, when starting the simulation from different initial configurations of the systems, the results are not changed significantly, when performed for 1248 ps. This study carried on FBPase‐AMP mimics corroborates well with our previous successful demonstration of requirement of simulation time for solvation studies, both by conventional and ab initio FEP. The establishment of aforementioned criteria of simulation length serves a useful benchmark in drug design efforts using FEP methodologies, to draw a meaningful and unequivocal conclusion. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011     

Experimental and theoretical study of the complexation of the thallium cation with a hexaarylbenzene-based receptor

Abstract  

From extraction experiments in the two-phase water/nitrobenzene system and γ-activity measurements, the stability constant of a hexaarylbenzene-based receptor. Tl⁺ complex species dissolved in nitrobenzene saturated with water was determined. By using the quantum-mechanical density functional level of theory calculations, the most probable structure of this complex was derived.     

On the local fractional wave equation in fractal strings

The key aim of the present study is to attain nondifferentiable solutions of extended wave equation by making use of a local fractional derivative describing fractal strings by applying local fractional homotopy perturbation Laplace transform scheme. The convergence and uniqueness of the obtained solution by using suggested scheme is also examined. To determine the computational efficiency of offered scheme, some numerical examples are discussed. The results extracted with the aid of this technique verify that the suggested algorithm is suitable to execute, and numerical computational work is very interesting.     

Amitriptylinium picrate: conformational disorder

In the structure of the title salt [systematic name: 3‐(10,11‐dihydro‐5H‐dibenzo[a,d][7]annulen‐5‐ylidene)‐N,N‐dimethylpropan‐1‐aminium 2,4,6‐trinitrophenolate] of a tricyclic antidepressant, C₂₀H₂₄N⁺·C₆H₂N₃O₇⁻, the dimethylaminopropyl subunit possesses a classical static conformational disorder. The central cycloheptadiene ring adopts a bent conformation that is intermediate between boat and chair forms, leading to a butterfly shape for the hetero‐tricyclic moiety. In a complementary fashion, donors from amitriptyline and acceptors from picrate form intermolecular C—H...O hydrogen bonds and N—H...O salt bridges. These hydrogen bonds cluster amitriptyline and picrate ions into a closed R₄⁴(36) hetero‐tetramer, whereas intermolecular C—H...π interactions between amitriptyline ions cluster them into homo‐dimers. Significant π–π stacking interactions are also observed between aromatic rings of amitriptyline and picrate, and these, combined with the C—H...π interactions, associate molecules into linear arrays along the [11] direction.     

Lattice vibronics of bcc phase metals (Ti,Zr and Hf) at higher temperatures

Ashcroft’s analytic bare ion pseudopotential form factor with a modified Hartree dielectric function has been employed to represent the temperature dependent interionic potential. This potential includes both direct ion-ion interaction and indirect ion-electron-ion interaction with and without the effects of ‘d’ bands, in some scantily studied complexbcc metals vizbcc Ti, Zr and Hf. The ab initio radial and tangential force constants extending out to 15th nearest neighbours are computed for the metals. The said potential is used for predicting the binding energy, elastic constants and phonon dispersion of the above mentioned metals and the results are satisfactorily compared with the corresponding measured data.     

Toroidal hopping of a single hole through the circularly-arrayed naphthyl groups in hexanaphthylbenzene cation radical

Synthesis of a dendritic (soluble) hexanaphthylbenzene derivative is described in which the six naphthyl groups are connected to the central benzene ring in a propeller-shaped arrangement. Observation of multiple oxidation waves in its cyclic voltammogram as well as an intense charge-resonance transition (extending beyond 1600 nm) in its cation radical, generated by laser-flash photolysis using photoexcited chloranil as an oxidant, suggests that a single hole is mobilized via electron transfer (or hopping) over six identical (circularly arrayed) redox centers.     

Kinetics of glass transition and thermal stability of?Se58Ge42?xPbx?(9≤x≤20) glasses

Se₅₈Ge_42−x Pb _x (9≤x≤20) glasses have been prepared using conventional melt quenching technique. Differential Scanning Calorimetric (DSC) measurements show single glass transition and double crystallization, which indicate the occurrence of phase separation in the samples. The phases present in the samples were identified using XRD. The kinetics of the glass transition has been studied in terms of the variation of glass transition temperature with composition and heating rate. In addition to this, activation energy of the glass transition (E _t ) has also been evaluated and its composition dependence is also investigated. The thermal stability of these glasses has been investigated using various stability criteria: Deiztal first glass criterion, ΔT, Saad and Poulain weighted thermal stability, H′ and the S-parameter. The values of these parameters were obtained using various characteristic temperatures such as the glass transition temperature, T _g , the onset temperature of crystallization, T _c , and the peak crystallization temperature, T _p . The values of stability parameters show that the phase corresponding to second crystallization is more stable than the phase corresponding to first one. The stability in terms of the lead (Pb) content has been determined considering the values of stability parameters of the phase corresponding to second peak. It was found that the stability increases with the lead content.     

A novel approach for protein identification from complex cell proteome using modified peptide mass fingerprinting algorithm

A unique peptide based search algorithm for identification of protein mixture using PMF is proposed. The proposed search algorithm utilizes binary search and heapsort programs to generate frequency chart depicting the unique peptides corresponding to all proteins in a proteome. The use of binary search program significantly reduces the time for frequency chart preparation to ～2 s for a proteome comprising ～23 000 proteins. The algorithm was applied to a three‐protein mixture identification, host cell protein (HCP) analysis, and a simulation‐generated data set. It was found that the algorithm could identify at least one unique peptide of a protein even in the presence of fourfold higher concentration of another protein. In addition, two HCPs that are known to be difficult to remove were missed by MS/MS approach and were exclusively identified using the presented algorithm. Thus, the proposed algorithm when used along with standard proteomic approaches present avenues for enhanced protein identification efficiency, particularly for applications such as HCP analysis in biopharmaceutical research, where identification of low‐abundance proteins are generally not achieved due to dynamic range limitations between the target product and HCPs.