Augmenting Basin-Hopping With Techniques From Unsupervised Machine Learning: Applications in Spectroscopy and Ion Mobility

Zhou, Chao; Ieritano, Christian; Hopkins, W. Scott

doi:10.3389/fchem.2019.00519

Cited by 21 publications

(18 citation statements)

References 94 publications

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“…To explore the potential energy surface of each tautomer, a custom basin hopping (BH) algorithm was employed. − Dihedral angles were randomly distorted by an angle −15 ° < ϕ < 15 ° , and molecular energies were calculated using the UFF forcefield . In total, ca.…”

Section: Theoretical Calculationsmentioning

confidence: 99%

“…20,000 structures were sampled by the BH algorithm for each prototropic isomer. Unique conformers, as determined based on energetic and geometric similarities, were further optimized using the B3LYP functional and 6-311++g(d,p) basis set as implemented in Gaussian 16 and including Grimme dispersion corrections (D3) . Implicit solvation studies were conducted to investigate the ion behavior in MeCN-modified environments.…”

Section: Theoretical Calculationsmentioning

confidence: 99%

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UVPD Spectroscopy of Differential Mobility-Selected Prototropic Isomers of Rivaroxaban

et al. 2021

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Two ion populations of protonated Rivaroxaban, [C 19 H 18 ClN 3 O 5 S + H] + , are separated under pure N 2 conditions using differential mobility spectrometry prior to characterization in a hybrid triple quadrupole linear ion trap mass spectrometer. These populations are attributed to bare protonated Rivaroxaban and to a proton-bound Rivaroxaban−ammonia complex, which dissociates prior to mass-selecting the parent ion. Ultraviolet photodissociation (UVPD) and collision-induced dissociation (CID) studies indicate that both protonated Rivaroxaban ion populations are comprised of the computed global minimum prototropic isomer. Two ion populations are also observed when the collision environment is modified with 1.5% (v/v) acetonitrile. In this case, the protonated Rivaroxaban ion populations are produced by the dissociation of the ammonium complex and by the dissociation of a proton-bound Rivaroxaban−acetonitrile complex prior to mass selection. Again, both populations exhibit a similar CID behavior; however, UVPD spectra indicate that the two ion populations are associated with different prototropic isomers. The experimentally acquired spectra are compared with computed spectra and are assigned to two prototropic isomers that exhibit proton sharing between distal oxygen centers.

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Section: Theoretical Calculationsmentioning

confidence: 99%

Section: Theoretical Calculationsmentioning

confidence: 99%

UVPD Spectroscopy of Differential Mobility-Selected Prototropic Isomers of Rivaroxaban

et al. 2021

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“…Candidate structures were then carried forward for pre-optimization at the semiempirical PM7 level of theory , and subsequently sorted based on cosine similarities. For details on cosine similarities, see ref . Unique conformers within 50 kJ mol –1 of the PM7 global minimum were then treated at the B3LYP-D3/6-31++G(d,p) level of theory.…”

Section: Methodsmentioning

confidence: 99%

Determining Collision Cross Sections from Differential Ion Mobility Spectrometry

et al. 2021

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The experimental determination of ion-neutral collision cross sections (CCSs) is generally confined to ion mobility spectrometry (IMS) technologies that operate under the so-called low-field limit or those that enable empirical calibration strategies (e.g., traveling wave IMS; TWIMS). Correlation of ion trajectories to CCS in other non-linear IMS techniques that employ dynamic electric fields, such as differential mobility spectrometry (DMS), has remained a challenge since its inception. Here, we describe how an ion’s CCS can be measured from DMS experiments using a machine learning (ML)-based calibration. The differential mobility of 409 molecular cations (m/z: 86–683 Da and CCS 110–236 Å2) was measured in a N2 environment to train the ML framework. Several open-source ML routines were tested and trained using DMS-MS data in the form of the parent ion’s m/z and the compensation voltage required for elution at specific separation voltages between 1500 and 4000 V. The best performing ML model, random forest regression, predicted CCSs with a mean absolute percent error of 2.6 ± 0.4% for analytes excluded from the training set (i.e., out-of-the-bag external validation). This accuracy approaches the inherent statistical error of ∼2.2% for the MobCal-MPI CCS calculations employed for training purposes and the <2% threshold for matching literature CCSs with those obtained on a TWIMS platform.

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“…The reasonability and similarity of the new structure should be checked and then optimized by the xTB method. For the acceptance of the newly distorted structure, the previously suggested criteria by Zhou et al are applied here ( Zhou et al, 2019 ). And the NKCS program also integrates the interface of Gaussian computing software ( Frisch et al, 2009 ) to perform high-level structure optimization and frequency calculation for the selected isomers by the BH algorithm.…”

Section: Methodsmentioning

confidence: 99%

Search for Global Minimum Structures of P2n+1+ (n = 1–15) Using xTB-Based Basin-Hopping Algorithm

Zhou

Cui

et al. 2021

Front. Chem.

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A new program for searching global minimum structures of atomic clusters using basin-hopping algorithm based on the xTB method was developed here. The program can be performed with a much higher speed than its replacement directly based on DFT methods. Considering the structural varieties and complexities in finding their global minimum structures, phosphorus cluster cations were studied by the program. The global minimum structures of cationic P2n+1+ (n = 1–15) clusters are determined through the unbiased structure searching method. In the last step, further DFT optimization was performed for the selected isomers. For P2n+1+ (n = 1–4, 7), the found global minimum structures are in consistent with the ones previously reported; while for P2n+1+ (n = 5, 6, 8–12), newly found isomers are more energy-favorable than those previously reported. And those for P2n+1+ (n = 13–15) are reported here for the first time. Among them, the most stable isomers of P2n+1+ (n = 4–6, 9) are characterized by their C3v, Cs, C2v and Cs symmetry, in turn. But those of P2n+1+ (n = 7, 8, 10–12), no symmetry has been identified. The most stable isomers of P29+ and P31+ are characterized by single P-P bonds bridging units inside the clusters. Further analysis shows that the pnicogen bonds play an important role in the stabilization of these clusters. These results show that the new developed program is effective and robust in searching global minimum structures for atom clusters, and it also provides new insights into the role of pnicogen bonds in phosphorus clusters.

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Augmenting Basin-Hopping With Techniques From Unsupervised Machine Learning: Applications in Spectroscopy and Ion Mobility

Cited by 21 publications

References 94 publications

UVPD Spectroscopy of Differential Mobility-Selected Prototropic Isomers of Rivaroxaban

UVPD Spectroscopy of Differential Mobility-Selected Prototropic Isomers of Rivaroxaban

Determining Collision Cross Sections from Differential Ion Mobility Spectrometry

Search for Global Minimum Structures of P2n+1+ (n = 1–15) Using xTB-Based Basin-Hopping Algorithm

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