Muhamad A. Martoprawiro

A first principles study of fluorescence quenching in rhodamine B dimers: how can quenching occur in dimeric species?

Rhodamine B (RhB) is widely used in chemistry and biology due to its high fluorescence quantum yield. In high concentrations, the quantum yield of fluorescence decreases considerably which is attributed to the formation of RhB dimers. In the present work, a possible mechanism of fluorescence quenching in RhB dimers is investigated with the use of time-dependent density functional theory (TD-DFT). The excited states of monomeric and dimeric RhB species have been studied both in the gas phase and in solution with the use of the TD-BLYP/6-311G* method. Results of the calculations suggest that quenching can occur via an internal conversion to the charge-transfer singlet excited states, which can be followed by an intersystem crossing with the charge-transfer triplet states. A possibility to reduce the loss of the fluorescence quantum yield is discussed.

Docking Interaction of Protein Tyrosine Phosphatase and Complex Chromium(III) Nicotinate Compounds

Docking simulation is important in the process of drug design, mainly used for the prediction of interactions receptor(protein)–substrate. This study aims to understand the interaction between Chromium(III) nicotinate [Cr(O-nic)2(OH ) (H2O)3] and [Cr(N-nic)2(OH )(H2O)3] with the position of trans and cis as a substrate with receptors Protein Tyrosine Phosphatase(PTP). The chromium(III) nicotinic complexes an antidiabetic supplement that have been demonstrated in vitro, to determine the role of chromium(III) nicotinic as a supplement antidiabetic learned through the docking mechanism. The optimization of the complex structure of chromium(III) nicotinic using Gaussian 09, the docking process is performed using Autodock Vina. The docking results showed that trans[Cr(O-nic)2(OH )(H2O)3] position interact with Leu13, Gly14, Cys17, Arg18, Trp49 and Asn50 with the interaction energy is -6.5 kcal/mol. As for the structure model cis[Cr(O-nic)2(OH )(H2O)3] have 6.1 kcal/mol interaction energy and the amino acid Ile16, Trp49, Asn50, Arg53, Asp56 and Tyr131. The similar things at model of N-coordinated to Cr with trans[Cr(N-nic)2(OH )(H2O)3] position interact with amino acids Leu13, Ser47, Trp49, Asn50 and Tyr131 the interaction energy is -6.5 kcal/mol. The ONIOM calculation showed the bond between the complexes of chromium(III) nicotinic with PTP is hydrogen bonding. The best interactions with the receptor are the structure model trans[Cr(O-nic)2(OH )(H2O)3] with the lowest interaction energy interaction.

Profile of students’ comprehension of 3D molecule representation and its interconversion on chirality

This study aims at describing (1) students’ level comprehension; (2) factors causing difficulties to 3D comprehend molecule representation and its interconversion on chirality. Data was collected using multiple-choice test consisting of eight questions. The participants were required to give answers along with their reasoning. The test was developed based on the indicators of concept comprehension. The study was conducted to 161 college students enrolled in stereochemistry topic in the odd semester (2014/2015) from two LPTK (teacher training institutes) in Bandar Lampung and Gorontalo, and one public university in Bandung. The result indicates that college students’ level of comprehension towards 3D molecule representations and its inter-conversion was 5% on high level, 22 % on the moderate level, and 73 % on the low level. The dominant factors identified as the cause of difficulties to comprehend 3D molecule representation and its interconversion were (i) the lack of spatial awareness, (ii) violation of ...

Formation of Bonded Exciplex in the Excited States of Dicyanoanthracene-Pyridine System: Time Dependent Density Functional Theory Study

Strong quenching of fluorescence was recently observed in pyridine solutions of 9,10-dicyanoanthracene chromophore. It was hypothesized that quenching may be attributed to the formation of bound charge transfer complexes in the excited states of the molecules. In this work, using time-dependent density functional calculations, we investigate the possibility of formation of bonded exciplex states between DCA and pyridine molecules. On the basis of theoretical calculations, it is proposed that a partial electron transfer occurs in the lowest excited state of the dicyanoanthracene-pyridine system which leads to the formation of bonded exciplex species and to quenching of fluorescence from dicyanoanthracene.

The Role of Electrostatic Interactions on Klentaq1 Insight for Domain Separation

We investigated the relationship between the thermostability of Klentaq1 and factors stabilizing interdomain interactions. When thermal adaptation of Klentaq1 was analyzed at the atomic level, the protein was stable at 300 and 350 K. It gradually unfolded at 373 K and almost spontaneously unfolded at 400 K. Domain separation was induced by disrupting electrostatic interactions in two salt bridges formed by Lys354-Glu445 and Asp371-Arg435 on the interface domain. The role of these interactions in protein stability was evaluated by comparing free energy solvation (ΔΔGsolv) between wild type and mutants. Substitution of Asp371 by Glu or Asn, and also Glu445 by Asn resulted in a positive value of ΔΔGsolv, suggesting that mutations destabilized the protein structure. Nevertheless, substitution of Glu445 by Asp gave a negative value to ΔΔGsolv reflecting increasing protein stability. Our results demonstrate that interactions at the interface domains of Klentaq1 are essential factors correlated with the Klentaq1 thermostability.

Modeling ionic conduction in γ-Bi 2 VO 5.5

?-Bi2VO5.5 family oxides has potential to play important role in solid oxide fuel cell, especially as the electrolyte due to their high ionic conductivity. In this work, oxide conduction in γ-Bi2VO5.5 is modeled based on bond valence sum (BVS) method. In γ-Bi2VO5.5, there are oxide vacancies at the equatorial position in the perovskite-like layers. These vacancies can facilitate oxide movement. The γ-Bi2VO5.5 model was built in a primitive structure with the entire V coordination in one layer are tetrahedron and entire V coordination in the next layer are octahedron. Oxygen movement, based on BVS result, mainly occurs in equatorial site i.e. on [140] direction. The minimum achieved BVS value was 1.320, which is considered as a site that has large cavity and facilitates oxygen hopping.