FT-IR spectra of the anti-HIV nucleoside analogue d4T (Stavudine). Solid state simulation by DFT methods and scaling by different procedures

Palafox, M. Alcolea; Kattan, D.; Afseth, Nils Kristian

doi:10.1016/j.molstruc.2017.12.079

Cited by 4 publications

(2 citation statements)

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“…These procedures inherently lead to further improvements in the scaled frequencies as the scaling changes depending on the different spectral regions, that is, the same scaling factor value is not applied to all frequencies. RMSE values ranging between 10 and 20 cm −1 have been found through application of these methods 85,87–92 . However, the parameters obtained in these approaches are highly dependent upon the molecules considered, limiting their broad applicability.…”

Section: History Of Uniform Scaling Factorsmentioning

confidence: 99%

Meta‐analysis of uniform scaling factors for harmonic frequency calculations

Trujillo

McKemmish

2021

WIREs Comput Mol Sci

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Vibrational frequency calculations performed under the harmonic approximation are widespread across chemistry. However, it is well‐known that the calculated harmonic frequencies tend to systematically overestimate experimental fundamental frequencies; a limitation commonly overcome with multiplicative scaling factors. In practice, multiplicative scaling factors are derived for each individual model chemistry choice (i.e., a level of theory and basis set pair), where performance is judged by, for example, the root‐mean square error (RMSE) between the predicted scaled and experimental frequencies. However, despite the overwhelming number of scaling factors reported in the literature and model chemistry approximations available, there is little guidance for users on appropriate model chemistry choices for harmonic frequency calculations. Here, we compile and analyze the data for 1495 scaling factors calculated using 141 levels of theory and 109 basis sets. Our meta‐analysis of this data shows that scaling factors and RMSE approach convergence with only hybrid functionals and double‐zeta basis sets, with anharmonicity error already dominating model chemistry errors. Noting inconsistent data and the lack of independent testing, we can nevertheless conclude that a minimum error of 25 cm−1—arising from insufficiently accurate treatment of anharmonicity—is persistent regardless of the model chemistry choice. Based on the data we compiled and cautioning the need for a future systematic benchmarking study, we recommend ωB97X‐D/def2‐TZVP for most applications and B2PLYP/def2‐TZVPD for superior intensity predictions. With a smaller benchmark set, direct comparison prefers ωB97X‐D/6‐31G* to B3LYP/6‐31G*. This article is categorized under: Electronic Structure Theory > Density Functional Theory Theoretical and Physical Chemistry > Spectroscopy

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Section: History Of Uniform Scaling Factorsmentioning

confidence: 99%

Meta‐analysis of uniform scaling factors for harmonic frequency calculations

Trujillo

McKemmish

2021

WIREs Comput Mol Sci

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“…All the simulations have been performed using the AMOEBA force fields, as implemented in the Tinker 8.6.1 software. In particular, we present our studies of thymidine in water, as parametrized in the AMOEBABIO18 force field, while we used AMOEBA09 parameters to model the N , N -DMF solvent, since it is not present in AMOEBABIO18. , For both solvents, we inserted the thymidine molecules in a cubic box whose sides measured 30 Å, as represented in Figure . In all calculations, the periodic boundary conditions are fully considered, using the particle mesh Ewald (PME) scheme for the long-range interactions. , …”

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confidence: 99%

Quantum Vibrational Spectroscopy of Explicitly Solvated Thymidine in Semiclassical Approximation

Gabas

Conte

Ceotto

2022

J. Phys. Chem. Lett.

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In this paper, we demonstrate the possibility to perform spectroscopy simulations of solvated biological species taking into consideration quantum effects and explicit solvation. We achieve this goal by interfacing our recently developed divide-and-conquer approach for semiclassical initial value representation molecular dynamics with the polarizable AMOEBABIO18 force field. The method is applied to the study of solvation of the thymidine nucleoside in two different polar solvents, water and N , N -dimethylformamide. Such systems are made of up to 2476 atoms. Experimental evidence concerning the different behavior of thymidine in the two solvents is well reproduced by our study, even though quantitative estimates are hampered by the limited accuracy of the classical force field employed. Overall, this study shows that semiclassically approximate quantum dynamical studies of explicitly solvated biological systems are both computationally affordable and insightful.

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