Dataset Information

Dimethylsulfoxide (DMSO) clusters dataset: DFT relative energies, non-covalent interactions, and cartesian coordinates.

ABSTRACT: Theoretical understanding of dimethylsulfoxide (DMSO) liquid depends on the understanding of the DMSO clusters. In this work, we provide the structures and the energetics of the DMSO clusters. The structures have been generated using ABCluster and further optimized at the MP2/aug-cc-pVDZ level of theory. The final structures have been optimized at two different levels of theory: PW6B95D3/aug-cc-pVDZ and ω B97XD/aug-cc-pVDZ. The Cartesian coordinates of the structures optimized at the MP2/aug-cc-pVDZ level of theory are also reported. The relative energies of the structures can be used to locate the most favorable structures of the DMSO clusters. The Cartesian coordinates of the structures can be used for further investigations on DMSO clusters. In addition, we report the data related to the quantum theory of atoms in molecule (QTAIM) analysis of the investigated clusters. The QTAIM data reported in this work can be used to understand and determine the nature of non-covalent interactions in DMSO clusters. For further reading and discussion on the data reported here, please report to the original manuscript Malloum and Conradie (2022) [1].

SUBMITTER: Malloum A

PROVIDER: S-EPMC8933536 | biostudies-literature | 2022 Jun

REPOSITORIES: biostudies-literature

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Dimethylsulfoxide (DMSO) clusters dataset: DFT relative energies, non-covalent interactions, and cartesian coordinates.

Malloum Alhadji A Conradie Jeanet J

Data in brief 20220307

Theoretical understanding of dimethylsulfoxide (DMSO) liquid depends on the understanding of the DMSO clusters. In this work, we provide the structures and the energetics of the DMSO clusters. The structures have been generated using ABCluster and further optimized at the MP2/aug-cc-pVDZ level of theory. The final structures have been optimized at two different levels of theory: PW6B95D3/aug-cc-pVDZ and ω B97XD/aug-cc-pVDZ. The Cartesian coordinates of the structures optimized at the MP2/aug-cc- ...[more]

PMID: 35313495

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Project description:BackgroundDiagnosis of infectious diseases now benefits from advancing technology to perform multiplex analysis of a growing number of variables. These advances enable simultaneous surveillance of markers characterizing species and strain complexity, mutations associated with drug susceptibility, and antigen-based polymorphisms in relation to evaluation of vaccine effectiveness. We have recently developed assays detecting single nucleotide polymorphisms (SNPs) in the P. falciparum genome that take advantage of post-PCR ligation detection reaction and fluorescent microsphere labeling strategies. Data from these assays produce a spectrum of outcomes showing that infections result from single to multiple strains. Traditional methods for distinguishing true positive signal from background can cause false positive diagnoses leading to incorrect interpretation of outcomes associated with disease treatment.ResultsFollowing analysis of Plasmodium falciparum dihydrofolate reductase SNPs associated with resistance to a commonly used antimalarial drug, Fansidar (Sulfadoxine/pyrimethamine), and presumably neutral SNPs for parasite strain differentiation, we first evaluated our data after setting a background signal based on the mean plus three standard deviations for known negative control samples. Our analysis of single allelic controls suggested that background for the absent allele increased as the concentration of the target allele increased. To address this problem, we introduced a simple change of variables from customary (X,Y) (Cartesian) coordinates to planar polar coordinates (X = rcos(theta), Y = rsin(theta)). Classification of multidimensional fluorescence signals based on histograms of angular and radial data distributions proved more effective than classification based on Cartesian thresholds. Comparison with known diallelic dilution controls suggests that histogram-based classification is effective for major:minor allele concentration ratios as high as 10:1.ConclusionWe have observed that the diallelic SNP data resulting from analysis of P. falciparum mutations is more accurately diagnosed when a simple polar transform of the (X,Y) data into (r,theta) is used. The development of high through-put methods for genotyping P. falciparum SNPs and the refinement of analytical approaches for evaluating these molecular diagnostic results significantly advance the evaluation of parasite population diversity and antimalarial drug resistance.

Project description:A vast number of non-covalent interaction energies at the counterpoise corrected CCSD(T) level have been collected from the literature to build a diverse new dataset. The whole dataset, which consists of 2027 CCSD(T) energies, includes most of the published data at this level. A large subset of the data was then used to train a novel, B3LYP specific, empirical correction scheme for non-covalent interactions and basis set superposition error (abbreviated as B3LYP-MM). Results obtained with our new correction scheme were directly compared to benchmark results obtained with B3LYP-D3(1) and M06-2X(2) (two popular density functions designed specifically to accurately model non-covalent interactions). For non-covalent complexes dominated by dispersion or dipole-dipole interactions all three tested methods give accurate results with the medium size aug-cc-pVDZ(3-6) basis set with MUE's of 0.27 (B3LYP-MM), 0.32 (B3LYP-D3) and 0.47 kcal/mol (M06-2X) (with explicit counterpoise corrections). These results validate both B3LYP-D3 and M06-2X for interactions of this type using a much larger data set than was presented in prior work. However, our new dispersion correction scheme shows some clear advantages for dispersion and dipole-dipole dominated complexes with the small LACVP* basis set, which is very popular in use due to its low associated computational cost: The MUE for B3LYP-MM with the LACVP* basis set for this subset of complexes (without explicit counterpoise corrections) is only 0.28 kcal/mol, compared to 0.65 kcal/mol for M06-2X or 1.16 kcal/mol for B3LYP-D3. Additionally, our new correction scheme also shows major improvements in accuracy for hydrogen-bonded systems and for systems involving ionic interactions, for example cation-π interactions. Compared to B3LYP-D3 and M06-2X, we also find that our new B3LYP-MM correction scheme gives results of higher or equal accuracy for a large dataset of conformer energies of di- and tripeptides, sugars, and cysteine.

Dataset Information

Dimethylsulfoxide (DMSO) clusters dataset: DFT relative energies, non-covalent interactions, and cartesian coordinates.

Publications

Dimethylsulfoxide (DMSO) clusters dataset: DFT relative energies, non-covalent interactions, and cartesian coordinates.

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