Electrically polarized valence basis sets for the SBKJC effective core potential developed for calculations of dynamic polarizabilities and Raman intensities

Vidal, Luciano N.; Vazquez, Pedro A. M.

doi:10.1007/s00214-012-1111-4

Cited by 8 publications

(6 citation statements)

References 41 publications

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“…Taking into account benchmark studies available in the literature, for both IR intensities 154,156,157,166,167 and Raman activities, 155,[166][167][168][169][170][171] we set up two benchmark sets considering small closed-and open-shell molecules with a variety of single and multiple bonds (benchmark set VIB67) and a few selected medium-sized molecular systems which can be considered as representatives of important biomolecule building blocks (benchmark set VIBbio100), in both cases considering only molecular systems which contain atoms from the first two rows of periodic table. Thus, the VIB67 benchmark set is composed of 15 molecules, in total 67 fundamental vibrations (CH + , HF, NH, OH, CN, CO, NO, H 2 O, H 2 CO, H 2 CN, C 2 H 4 , CH 2 F 2 , CH 3 NH 2 , CH 3 OH, HCONH 2 and HCOOH); while the VIBbio100 benchmark set is composed of: furan, pyrrole, pyrimidine, glycine and phenyl radical, with over 100 fundamental vibrations.…”

Section: Thermodynamicsmentioning

confidence: 99%

Fully anharmonic IR and Raman spectra of medium-size molecular systems: accuracy and interpretation

Barone

Biczysko

Bloino

2014

Phys. Chem. Chem. Phys.

393

547

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Computation of full infrared (IR) and Raman spectra (including absolute intensities and transition energies) for medium- and large-sized molecular systems beyond the harmonic approximation is one of the most interesting challenges of contemporary computational chemistry. Contrary to common beliefs, low-order perturbation theory is able to deliver results of high accuracy (actually often better than those issuing from current direct dynamics approaches) provided that anharmonic resonances are properly managed. This perspective sketches the recent developments in our research group toward the development of a robust and user-friendly virtual spectrometer rooted in second-order vibrational perturbation theory (VPT2) and usable also by non-specialists essentially as a black-box procedure. Several examples are explicitly worked out in order to illustrate the features of our computational tool together with the most important ongoing developments.

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Section: Thermodynamicsmentioning

confidence: 99%

Fully anharmonic IR and Raman spectra of medium-size molecular systems: accuracy and interpretation

Barone

Biczysko

Bloino

2014

Phys. Chem. Chem. Phys.

393

547

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“…For geometry optimization with GAMESS-US, − we employed the hybrid DFT method B3LYP and electrically polarized basis set SBKJC ECP. The SBKJC basis set is particularly designed to handle metals of groups 14 (C–Sn), 15 (N–Sb), 16 (O–Te), and 17 (F–I) that describe the unperturbed system using the valence double-zeta pseudopotential basis set proposed by Stevens and co-workers. − The first step of QM calculations generated three fingerprint files (standard, small, and large models) for each model (1–3), which contain information about the metal ion and ligating atoms whose parameters do not exist in the AMBER force field. To find a local minimum of the small and large models, a similar basis set was employed for geometry optimization and force constant calculations, which was then visualized using visual MD (VMD) to reaffirm bond coordination to metals …”

Section: Methodsmentioning

confidence: 99%

“…The SBKJC basis set derived by Stevens and co-workers encompassing the valence double-zeta potential set coupled with ECP has been employed in this study to optimize Bi-and Sb-containing compounds. SBKJC particularly deals with large sets of systems comprising elements of higher period numbers covering atoms from mostly groups 46 The current study, however, proposes Bi-containing compounds with pentagonal geometries for further analysis, which if/must be considered for optimization with methods like SBKJC ECP with pseudopotential referred to as pSBKJC, will effectively lower the computational cost expended for heavy nuclei comprising a large number of electrons.…”

Section: ■ Resp Chargesmentioning

confidence: 97%

Quantum Dynamics and Bi Metal Force Field Parameterization Yielding Significant Antileishmanial Targets

Zaman

Azam

2023

J. Chem. Inf. Model.

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Amid emerging drug resistance to metal inhibitors, high toxicity, and onerous drug delivery procedures, the computational design of alternate formulations encompassing functional metal-containing compounds greatly relies on large-scale atomistic simulations. Simulations particularly with Au(I), Ag, Bi(V), and Sb(V) pose a major challenge to elucidate their molecular mechanism due to the absence of force field parameters. This study thus quantum mechanically derives force field parameters of Bi(V) as an extension of the previous experimental study conducted on heteroleptic triorganobismuth(V) biscarboxylates of type [BiR3(O2CR′)2]. We have modeled two organo-bismuth(V) carboxylates, which are optimized and parameterized along with the famous pentavalent antimonial drug: meglumine antimoniate using quantum mechanics original Seminarian methods with the SBKJC effective core potential (ECP) basis set. Furthermore, molecular dynamics (MD) simulations of bismuth- and antimony-containing compounds in complex with two enzymes, trypanothione synthetase-amidase (TSA) and trypanothione reductase, are performed to target the (T(SH)2) pathway at multiple points. MD simulations provide novel insights into the binding mechanism of TSA and highlight the role of a single residue Arg569 in modulating the ligand dynamics. Moreover, the presence of an ortho group in a ligand is emphasized to facilitate interactions between Arg569 and the active site residue Arg313 for higher inhibitory activity of TSA. This preliminary generation of parameters specific to bismuth validated by simulations in replica will become a preamble of future computational and experimental research work to open avenues for newer and suitable drug targets.

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“…The main required information is obtained from the interatomic distance matrix, tensors of inertia or directly from the atomic coordinates. They were implemented in our program PLACZEK to enable the automatic exploitation of the point group symmetry in infrared and Raman spectra calculations.…”

Section: Introductionmentioning

confidence: 99%

Algorithms for computer detection of symmetry elements in molecular systems

Beruski

Vidal

2013

J Comput Chem

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Simple procedures for the location of proper and improper rotations and reflexion planes are presented. The search is performed with a molecule divided into subsets of symmetrically equivalent atoms (SEA) which are analyzed separately as if they were a single molecule. This approach is advantageous in many aspects. For instance, in those molecules that are symmetric rotors, the number of atoms and the inertia tensor of the SEA provide one straight way to find proper rotations of any order. The algorithms are invariant to the molecular orientation and their computational cost is low, because the main information required to find symmetry elements is interatomic distances and the principal moments of the SEA. For example, our Fortran implementation, running on a single processor, took only a few seconds to locate all 120 symmetry operations of the large and highly symmetrical fullerene C720, belonging to the Ih point group. Finally, we show how the interatomic distances matrix of a slightly unsymmetrical molecule is used to symmetrize its geometry.

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Electrically polarized valence basis sets for the SBKJC effective core potential developed for calculations of dynamic polarizabilities and Raman intensities

Cited by 8 publications

References 41 publications

Fully anharmonic IR and Raman spectra of medium-size molecular systems: accuracy and interpretation

Fully anharmonic IR and Raman spectra of medium-size molecular systems: accuracy and interpretation

Quantum Dynamics and Bi Metal Force Field Parameterization Yielding Significant Antileishmanial Targets

Algorithms for computer detection of symmetry elements in molecular systems

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