Cis/trans energetics in epoxide, thiirane, aziridine and phosphirane containing cyclopentanols: Effects of intramolecular OH···O,S,N and P contacts

c 2019 by the authors A recent computational analysis of the stabilizing intramolecular OH···O contact in 1,2-dialkyl-2,3-epoxycyclopentanol diastereomers has been extended to thiiriane, aziridine and phosphirane analogues. Density functional theory (DFT), second-order Møller-Plesset perturbation theory (MP2) and CCSD(T) coupled-cluster computations with simple methyl and ethyl substituents indicate that electronic energies of the cis isomers are lowered by roughly 3 to 4 kcal mol−1 when the OH group of these cyclopentanol systems forms an intramolecular contact with the O, S, N or P atom on the adjacent carbon. The results also suggest that S and P can participate in these stabilizing intramolecular interactions as effectively as O and N in constrained molecular environments. The stabilizing intramolecular OH···O, OH···S, OH···N and OH···P contacts also increase the covalent OH bond length and significantly decrease the OH stretching vibrational frequency in every system with shifts typically on the order of −41 cm−

Co-Localization of DNA i-Motif-Forming Sequences and 5-Hydroxymethyl-cytosines in Human Embryonic Stem Cells

G-quadruplexes (G4s) and i-motifs (iMs) are tetraplex DNA structures. Sequences capable of forming G4/iMs are abundant near the transcription start sites (TSS) of several genes. G4/iMs affect gene expression in vitro. Depending on the gene, the presence of G4/iMs can enhance or suppress expression, making it challenging to discern the underlying mechanism by which they operate. Factors affecting G4/iM structures can provide additional insight into their mechanism of regulation. One such factor is epigenetic modification. The 5-hydroxymethylated cytosines (5hmCs) are epigenetic modifications that occur abundantly in human embryonic stem cells (hESC). The 5hmCs, like G4/iMs, are known to participate in gene regulation and are also enriched near the TSS. We investigated genomic co-localization to assess the possibility that these two elements may play an interdependent role in regulating genes in hESC. Our results indicate that amongst 15,760 G4/iM-forming locations, only 15% have 5hmCs associated with them. A detailed analysis of G4/iM-forming locations enriched in 5hmC indicates that most of these locations are in genes that are associated with cell differentiation, proliferation, apoptosis and embryogenesis. The library generated from our analysis is an important resource for investigators exploring the interdependence of these DNA features in regulating expression of selected genes in hESC

Observation of the Low-Frequency Spectrum of the Water Trimer as a Sensitive Test of the Water-Trimer Potential and the Dipole-Moment Surface

© 2020 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA. Intermolecular interactions in bulk water are dominated by pairwise and non-pairwise cooperative interactions. While accurate descriptions of the pairwise interactions are available and can be tested by precise low-frequency spectra of the water dimer up to 550 cm−1, the same does not hold for the three-body interactions. Here, we report the first comprehensive spectrum of the water trimer in the frequency region from 70 to 620 cm−1 using helium-nanodroplet isolation and free-electron lasers. By comparison to accompanying high-level quantum calculations, the experimentally observed intermolecular bands can be assigned. The transition frequencies of the degenerate translation, the degenerate in-plane and the non-degenerate out-of-plane libration, as well as additional bands of the out-of-plane librational mode are reported for the first time. These provide a benchmark for state-of-the-art water potentials and dipole-moment surfaces, especially with respect to three-body interactions

A Raman spectroscopic and computational study of new aromatic pyrimidine-based halogen bond acceptors

© 2019 by the authors. Two new aromatic pyrimidine-based derivatives designed specifically for halogen bond directed self-assembly are investigated through a combination of high-resolution Raman spectroscopy, X-ray crystallography, and computational quantum chemistry. The vibrational frequencies of these new molecular building blocks, pyrimidine capped with furan (PrmF) and thiophene (PrmT), are compared to those previously assigned for pyrimidine (Prm). The modifications affect only a select few of the normal modes of Prm, most noticeably its signature ring breathing mode, ν1. Structural analyses afforded by X-ray crystallography, and computed interaction energies from density functional theory computations indicate that, although weak hydrogen bonding (C-H...O or C-H...N interactions) is present in these pyrimidine-based solid-state co-crystals, halogen bonding and π-stacking interactions play more dominant roles in driving their molecular-assembly

Fundamental vibrational frequencies of pnictogen (<i>Pn</i>) containing linear triatomic anions: OC<i>Pn</i>^- and SC<i>Pn</i>^- where <i>Pn</i> = N, P, As and Sb

The fundamental vibrational frequencies of the isolated OCAs− and SCAs− ions, as well as their heavier antimony analogues, are reported for the first time. A thorough analysis of basis set convergence of the bond lengths and harmonic vibrational frequencies, as well as the examination of anharmonic corrections, is conducted using the MP2 and CCSD(T) ab initio methods with robust basis sets for the OCPn− and SCPn− anions moving down the pnictogen series from Pn = N to Sb. Second-order vibrational perturbation theory (VPT2) and vibrational configuration interaction (VCI) theory are used to compute the fundamental vibrational frequencies of each triatomic anion approaching the MP2 and CCSD(T) complete basis set (CBS) limits. While fundamental vibrational frequencies have been reported for OCN− and SCN− in the gas phase, only experimental vibrational frequencies of the salts for the heavier pnictogen analogues (P and As) have been reported. Experimental Raman vibrational frequencies for OCAs− and SCAs− salts were found to be coincidentally in good agreement with the CCSD(T) VCI frequencies near the CBS limit, differing by at most 13 cm−1 from the former and 9 cm−1 from the latter. These modest differences are likely due to the presence of counter-ions and other environmental effects in the solid state, and the overall agreement between the salts and gas-phase frequencies is quite similar to that observed for the OCP− and SCP− ions.</p

COMPUTATIONAL AND SPECTROSCOPIC STUDY OF THE B-N DATIVE BOND IN AMMONIA BORANE

Author Institution: University of Mississippi, Department of Chemistry \&amp; Biochemistry, Oxford, MS 38677Ammonia borane is the archetypal small molecule employed to study dative bonds (also known as coordinate covalent or dipolar bonds) theoretically. We analyze the sensitivity of the B-N dative bond to method and basis set by computing the B-N bond length and the B-N stretching frequency. Our goal is to find the least computationally demanding method and basis set combination that yields trustworthy results. Previous researchers have demonstrated the inaccuracy of the B3LYP method for describing this type of bond. Here, we compare results using the M06-2X hybrid density functional with ab initio methods including MP2, CCSD, and CCSD(T) with different sized basis sets. We compare these results to experimental solid state and gas phase Raman spectra. Monomer calculations overestimate the B-N bond length and underestimate the B-N stretch in ammonia borane when compared to experimental values. However, calculations performed on clusters of ammonia borane molecules do a better job of reproducing the solid state experimental results. This agreement could be due to dihydrogen bonding between the ammonia borane molecules

Hydrocarbon/Water Interactions: Encouraging Energetics and Structures from DFT but Disconcerting Discrepancies for Hessian Indices

In this work, <i>ab initio</i> electronic structure computations have been used to systematically examine the structures and energetics of nine small hydrocarbon molecules interacting with water. Full geometry optimizations and harmonic vibrational frequency calculations were performed on 30 unique dimer configurations with the MP2 method and a triple-ζ correlation consistent basis set (cc-pVTZ for H and aug-cc-pVTZ for C and O, denoted haTZ). Three different estimates of the CCSD­(T) complete basis set (CBS) limit interaction energies were determined for all 30 MP2 optimized hydrocarbon/water structures, and they never deviate from their mean by more than 0.07 kcal mol^–1. MP2 and CCSD­(T) interaction energies are virtually identical (within 0.05 kcal mol^–1) for dimer configurations primarily exhibiting CH···O and OH···C type interactions, but MP2 overbinds appreciably in some dimers that exhibited OH···π type interactions, by as much as 0.3 to 0.4 kcal mol^–1 (or ≈10%) for the unsaturated cyclic hydrocarbons examined (1,3-cyclobutadiene, 1,3-cyclopentadiene, and benzene). Four density functional theory (DFT) methods (B3LYP, B97-D, ωB97X-D, and M06-2X) were also applied to all 30 systems with the haTZ basis set to compare optimized structures, energetics, and numbers of imaginary vibrational frequencies (n_<i>i</i>). The B97-D, ωB97X-D, and M06-2X functionals provide quite reasonable structures and energetics, which is consistent with other studies. This work, however, finds that all 4 DFT methods examined struggle to reliably characterize these potential energy surfaces (PESs). For example, the values of n_<i>i</i> from the DFT frequency calculations differed from the corresponding MP2 results for approximately one-third of the stationary points located