0000000001203534
AUTHOR
Julen Larrucea
Density functional study of Cu2+-phenylalanine complex under micro-solvation environment
Abstract We present an atomistic study carried out using density functional calculations including structural relaxations and Car–Parrinello Molecular Dynamics (CPMD) simulations, aiming to investigate the structures of phenylalanine-copper (II) ([Phe-Cu] 2+ ) complexes and their micro-solvation processes. The structures of the [Phe-Cu] 2+ complex with up to four water molecules are optimized using the B3LYP/6-311++G** model in gas phase to identify the lowest energy structures at each degree of solvation ( n = 0–4). It is found that the phenylalanine appears to be in the neutral form in isolated and mono-hydrated complexes, but in the zwitterionic form in other hydrated complexes (with n …
Structure and dynamics in liquid bismuth and Bin clusters: A density functional study
Density functional/molecular dynamics simulations with more than 500 atoms have been performed on liquid bismuth at 573, 773, 923, and 1023 K and on neutral Bi clusters with up to 14 atoms. There are similar structural patterns (coordination numbers, bond angles, and ring patterns) in the liquid and the clusters, with significant differences from the rhombohedral crystalline form. We study the details of the structure (structure factor, pair, and cavity distribution functions) and dynamical properties (vibration frequencies, diffusion constants, power spectra), and compare with experimental results where available. While the three short covalent bonds typical to pnictogens are characteristi…
Nucleus-driven crystallization of amorphous Ge2Sb2Te5: A density functional study
Early stages of nucleus-driven crystallization of the prototype phase change material Ge${}_{2}$Sb${}_{2}$Te${}_{5}$ have been studied by density functional/molecular dynamics simulations for amorphous samples (460 and 648 atoms) at 500, 600, and 700 K. All systems assumed a fixed cubic seed of 58 atoms and 6 vacancies. Crystallization occurs within 600 ps for the 460-atom system at 600 and 700 K, and signs of crystallization (nucleus growth, percolation) are present in the others. Crystallization is accompanied by an increase in the number of ``$ABAB$ squares'' ($A$: Ge, Sb, $B$: Te), and atoms of all elements move significantly. There is no evidence of cavity movement to the crystal-glass…
Polymorphism in phase-change materials: melt-quenched and as-deposited amorphous structures in Ge2Sb2Te5from density functional calculations
The as-deposited (AD) amorphous structure of the prototype phase change material Ge${}_{2}$Sb${}_{2}$Te${}_{5}$ (GST-225) has been studied by density functional calculations for a 648-atom sample generated by computer-aided deposition at 300 K. The AD sample differs from a melt-quenched (MQ) sample in essential ways: (1) Ge atoms are predominantly tetrahedrally coordinated, and (2) homopolar and Ge-Sb bonds are more common and reduce the number of $\mathit{ABAB}$ squares ($A=\mathrm{Ge}$, Sb; $B=\mathrm{Te}$), the characteristic building blocks of the material. The first observation resolves the contradiction between measured (EXAFS) and calculated Ge-Te bond lengths, and the latter explain…
Ordering the amorphous – Structures in PBD LED materials
Abstract The class of 2,5 disubstituted-1,3,4-oxadiazoles containing a biphenyl unit on one side is intensively used as electron transport materials to enhance the performance of organic light emitting diodes (OLEDs). In contrast to the ongoing research on these materials insights in their structure-property relationships are still incomplete. To overcome the structural tentativeness and ambiguities the crystal structures of 2-(4-biphenylyl)-5-(4-tert-butylphenyl)-1,3,4-oxadiazole, that of the related compound 2-(4-biphenylyl)-5-phenyl-1,3,4-oxadiazole and of 2-(4-biphenylyl)-5-(2,6-dimethylphenyl)-1,3,4-oxadiazole are determined. A comparison with the results of GAUSSIAN03 calculations and…
CPMD simulation of Cu2+ -- phenylalanine complex under micro-solvated environment
The study combines DFT calculations and CPMD simulations to investigate the structures of phenylalanine-copper (II) ([Phe-Cu]2+) complexes and the micro-solvation processes. ....It is found that the phenylalanine moiety appears to be in the neutral form in isolated and mono-hydrated complexes, but in the zwitterionic form in other hydrated complexes (with n no less than 2). .... The present CPMD simulations reveal that the maximum coordination of Cu2+ in the presence of the Phe ligand does not exceed four: the oxygen atoms from three water molecules and one carboxyl oxygen atom of Phe. Any excess water molecules will migrate to the second solvation shell. Moreover a unique structural motif …