Publications by authors named "Jose Manuel Vasquez-Perez"
J Chem Inf Model
February 2023
Article Synopsis
- The text introduces a more efficient algorithm for solving the near-congruence problem in rigid molecules and clusters using iterative assignment and alignment steps with biased costs.
- This new method enhances efficiency by up to 5 orders of magnitude compared to older, unbiased approaches and is capable of handling large systems with hundreds or thousands of atoms.
- The algorithm, available as an open-source Fortran library, can be utilized in global optimization techniques to identify local minima or basins in molecular structures.
J Chem Theory Comput
July 2022
Article Synopsis
- - This study examines how to optimize the shape and total spin of small iron clusters (Fe) using Simulated Annealing (SA) and DFTB theory, focusing on clusters ranging from 3 to 40 atoms.
- - The researchers allowed for a flexible total spin by adjusting the occupancy of spin densities during the SA process, leading to varied spin states throughout the simulations.
- - Their results showed that the optimized cluster structures closely matched previously reported geometries and magnetic moments, and they also computed binding energies to further validate their findings, noting few discrepancies likely due to competing magnetic states at high temperatures.
Article Synopsis
- The study focuses on the synthesis of two oligophenyleneimine pentamers, DAFCHO and FDACHO, which contain terminal aldehydes, using mechanochemistry methods and various diamines.*
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- The compounds were characterized using spectroscopy techniques (¹H and C-NMR, FT-IR, mass spectrometry) and displayed interesting photochromic properties in chloroform when exposed to sunlight, with notable energy band gap values measured.*
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- Electrochemical studies revealed their potential as organic semiconductors, with HOMO and LUMO values indicating favorable electronic properties, and findings were further supported by Density Functional Theory (DFT) calculations.*
Article Synopsis
- - The study focuses on understanding the chemical reactivity of metal clusters, which can be complex due to their unusual transition state structures.
- - Researchers used a special algorithm in the deMon2k code to identify transition states for small sodium clusters containing 6 to 10 atoms, integrating two different methods for better accuracy.
- - To link the transition states with minimum structures, intrinsic reaction coordinates were calculated, showcasing a method to investigate complex rearrangement processes in metal clusters.
J Chem Phys
September 2009
Article Synopsis
- This study focuses on neutral, cationic, and anionic sodium cluster heptamers using density functional theory to optimize their structures.
- New unexpected isomers close in energy to known ground state structures were discovered, particularly in neutral and cationic clusters, with one identified during molecular dynamics simulations at 300 K.
- A new structure alignment algorithm was introduced to analyze the evolution of these isomers at various temperatures, showcasing the effectiveness of 100 ps molecular dynamics simulations in exploring the energy landscape of these metallic clusters.
