1,720,964 research outputs found
Iterative Implementation of the Dipole Interaction Model for Atomic Polarizabilities
No full textABSTRACT Despite its name, the dipole interaction model (DIM) serves not only to adjust dipole moments due to atomic interactions but also to assess polarizabilities. Traditionally, polarizability calculations via DIM rely on matrix inversion, posing constraints on memory usage and computational time. Recent implementations have shown significant performance boosts by employing an iterative inversion solver, albeit reducing accuracy. In this paper, we present a direct approach for computing polarizabilities via iterative cycles, eliminating the need for matrix inversion. This allows for scaling up the model to hundreds of thousands of atoms without sacrificing precision, as often happens when simplifying the standard inversion procedure to reduce computational costs. Additionally, we have addressed memory issues associated with storing extensive arrays in standard implementations. Our advancement holds promise for diverse applications, providing an efficient method for exploring polarizabilities in various systems.Conselho Nacional de Desenvolvimento Científico e Tecnológico https://doi.org/10.13039/50110000359
Accurate atom–dipole interaction model for prediction of electro-optical properties : from van der Waals aggregates to covalently bonded clusters
No full textCrystal Field Effects on Atomic and Functional-Group Distributed Polarizabilities of Molecular Materials
No full textElectric charge and salting in/out effects on glucagon's dipole moments and polarizabilities using the GruPol database
No full textThis work demonstrates the use of the GruPol database to predict the functional group dipole moments and polarizabilities of glucagon in the presence of NaCl, simulating an electric charge distribution on the protein's backbone. A new feature of the database allows for the inclusion of ions on the protein backbone, effectively simulating a protein salt and predicting the impact on electrical properties. Glucagon was selected as a proof-of-concept molecule due to its relatively small chain, which enabled benchmarking against quantum mechanical calculations. Firstly, we simulated 70 different ionic configurations, varying the number of Na + and Cl − ions from zero to four NaCl moieties. Additionally, we investigated the effects of solvation under two distinct conditions: one involving just the peptide and water, and the other also including NaCl at a concentration of approximately 4.2 mol L −1 . Regarding the ab initio results, GruPol showed good accuracy, with an angular direction error of around 10° and a 15% difference in the magnitude of the dipole moments. However, the error in polarizability values was higher, most likely due to the lack of an augmented basis set in the ab initio quantum calculations (M06-HF/cc-pVDZ). The database entries were generated using the same functional along with the aug-cc-pVDZ basis set. In solution, a high ionic concentration lowered the overall dipole moment, while the main components of polarizability increased.Infrastruktura PL-Grid https://doi.org/10.13039/501100011089Fundação de Amparo à Pesquisa do Estado de Minas Gerais https://doi.org/10.13039/501100004901Conselho Nacional de Desenvolvimento Científico e Tecnológico https://doi.org/10.13039/50110000359
Distributed functional-group polarizabilities in polypeptides and peptide clusters toward accurate prediction of electro-optical properties of biomacromolecules
No full textPolarization and Dipole Moment Effects on Sigma‐Hole Potential in Tin(IV)‐Porphyrins
No full textAbstract This study investigates how electron‐withdrawing substitution, molecular polarization, and dipole moment influence the σ‐hole potential in six‐coordinate metalloporphyrins. To evaluate halogen bonding tendencies, we synthesized a series of five Sn(IV)‐5,10,15,20‐meso‐tetrakis(4‐iodophenyl)porphyrin complexes with various fluorinated phenolate axial ligands. Single‐crystal X‐ray diffraction analysis revealed distinct halogen‐bonded supramolecular motifs, which vary depending on the degree of fluorination at the axial ligands. Our findings highlight the critical role of ligand‐induced polarization and dipole moment variations in modulating the σ‐hole characteristics of the equatorial iodine atoms. Computational modelling showed that increased fluorine substitution reduces both the atomic dipole moments of fluorine and the polarizability of the central tin ion. However, despite these changes, the axial fluorination has a negligible effect on the σ‐hole potential at the iodine atoms. This limited influence is attributed to the orthogonal orientation between the porphyrin core and the peripheral phenyl rings, which suppresses resonance interactions. Overall, this work emphasizes the importance of understanding electronic effects at the molecular level, particularly in the design and formation of halogen‐bonded supramolecular architectures.Infrastruktura PL-Grid https://doi.org/10.13039/50110001108
Benchmark of a functional-group database for distributed polarizability and dipole moment in biomolecules
No full textApplication of group polarizability database towards better prediction of electric moments and electrostatic properties of biomolecules.The extraction of functional-group properties in condensed phases is very useful for predicting material behaviors, including those of biomaterials. For this reason, computational approaches based on partitioning schemes have been developed aiming at rapidly and accurately estimating properties from chemically meaningful building blocks. A comprehensive database of group polarizabilities and dipole moments is useful not only to predict the optical properties of biomacromolecules but also to improve molecular force fields focused on simulating biochemical processes. In this work we benchmark a database of distributed polarizabilities and dipole moments for functional groups extracted from a series of polypeptides. This allows reconstruction of a variety of relevant chemical environments. The accuracy of our database was tested to predict the electro-optical properties of larger peptides and also simpler amino acids for which density functional theory calculations at the M06-HF/aug-cc-pVDZ level of theory was chosen as the reference. This approach is reasonably accurate for the diagonal components of the polarizability tensor, with errors not larger than 15–20%. The anisotropy of the polarizability is predicted with smaller efficacy though. Solvent effects were included explicitly by surrounding the database entries by a box of water molecules whose distribution was optimized using the CHARMM force field.Fundação de Amparo à Pesquisa do Estado de Minas Gerais https://doi.org/10.13039/501100004901Infrastruktura PL-Grid https://doi.org/10.13039/50110001108
Unveiling GruPol: Predicting Electric and Electrostatic Properties of Macromolecules via the Building Block Approach
No full textIntriguing Reactivity of a 1,2‐Dihydrodialumane Towards Organic Azides – From a Terminal Diazido–Dialumane to Pendulum‐Clock‐Like Azide Bridging
No full textAbstract The reactivity of dihydro‐dialane with organic azides is described. Treatment of the hybrid ligand‐based dialane [(DNI{H}Al) 2 ] ( I ) (DNI = [3,3‐dimethyl‐2‐2‐methyl‐2‐(2,6‐diisopropylaniline)ethenyl]‐3H‐indolenine) with TMSN 3 (TMS = trimethylsilyl) at room temperature gives the first diazido‐dialane [(DNI{N 3 }Al) 2 ] ( 1 ). The transformation from here to a more stable aluminium‐tetrazole [DNIAl(NTMS) 2 N 2 ] ( 2 ) is established. The reaction of other RN 3 gives [(DNI{H}Al) 2 (κ 2 ‐N 3 R)] (R = Benzyl in 3 and 1‐Adamantyl in 4 ) with the azide in a μ‐bridging position between two aluminium atoms. Using 1 H NOESY/EXSY NMR spectroscopy, a positional exchange of the two TMS groups ( 2 ) via rotation of the tetrazole unit is observed. In contrast, compound 3 exhibits a pendulum‐clock‐like dynamic, with N α oscillating between the two aluminium atoms in solution. The reaction of dialane I with DippN 3 (Dipp = 2,6‐ i Pr 2 ‐C 6 H 3 ) gives the dialuminium amine [{DNI(H)Al} 2 (μ‐NDipp)] ( 5 ).Academic Computer Centre Cyfronet, AGH University of Science and Technology https://doi.org/10.13039/50110002167
Bemerkenswerte Reaktivität eines 1,2‐Dihydrodialans mit organischen Aziden – vom terminalen Diazido–Dialuman zur pendeluhrartigen Azidbrücke
No full textAcademic Computer Centre Cyfronet, AGH University of Science and Technology https://doi.org/10.13039/50110002167
- …
