Can 2‑X-Ethanols Form Intramolecular Hydrogen Bonds? Rosenberg, Robert E
The journal of physical chemistry. A, Molecules, spectroscopy, kinetics, environment, & general theory,
09/2019, Volume:
123, Issue:
35
Journal Article
Peer reviewed
For 2-X-ethanols, where X = F, OH, or NH2, the gauche conformer is favored over the trans conformer by at least 2 kcal/mol. Initially, this preference, ΔE, was attributed to an intramolecular ...hydrogen bond, IMHB, between the OH and X groups. Over the years, this conclusion has been challenged by two major arguments. One claim is that the entirety of ΔE can be accounted for by the gauche effect. Against this, calculations using five different methods show that the maximum contribution of the gauche effect to ΔE is less than 1 kcal/mol. A second argument employs the quantum theory of atoms in molecules to contend that the absence of a bond critical point (BCP) between the OH and X groups in 2-X-ethanols denotes the lack of an IMHB. By looking at the 2-X-ethanols at fixed XCCO torsional angles ranging from 0° to 60°, it is shown that the BCP criterion is inconsistent with other properties such as energy, bond lengths, and stretching frequencies. These inconsistencies are removed when the theory of noncovalent interactions is used. The IMHBs in 2-X-ethanols are found to be similar in form but smaller in magnitude than their intermolecular counterparts. This work concludes that 2-X-ethanols form IMHBs.
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IJS, KILJ, NUK, PNG, UL, UM
Fluorinated organic compounds are ubiquitous in the pharmaceutical and agricultural industries. To better discern the mode of action of these compounds, it is critical to understand the strengths of ...hydrogen bonds involving fluorine. There are only a few published examples of the strengths of these bonds. This study provides a high level ab initio study of inter- and intramolecular hydrogen bonds between RF and R′OH, where R and R′ are aryl, vinyl, alkyl, and cycloalkyl. Intermolecular binding energies average near 5 kcal/mol, while intramolecular binding energies average about 3 kcal/mol. Inclusion of zero-point energies and applying a counterpoise correction lessen the difference. In both series, modest increases in binding energies are seen with increased acidity of R′OH and increased electron donation of R in RF. In the intramolecular compounds, binding energy increases with the rigidity of the F–(C) n –OH ring. Inclusion of free energy corrections at 298 K results in exoergic binding energies for the intramolecular compounds and endoergic binding energies for the intermolecular compounds. Parameters such as bond lengths, vibrational frequencies, and atomic populations are consistent with formation of a hydrogen bond and with slightly stronger binding in the intermolecular cases over the intramolecular cases. However, these parameters correlated poorly with binding energies.
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IJS, KILJ, NUK, PNG, UL, UM
3.
Microsolvation of Fluoromethane Rosenberg, Robert E
The journal of physical chemistry. A, Molecules, spectroscopy, kinetics, environment, & general theory,
09/2016, Volume:
120, Issue:
38
Journal Article
Peer reviewed
Fluorinated organic compounds are ubiquitous in the pharmaceutical and agricultural industries. To better discern the mode of action of these compounds, it is critical to understand the potential for ...and strength of hydrogen bonds involving fluorine. It is known that CH3F forms a hydrogen bond with H2O in the gas phase but does not dissolve in bulk water. This paper examines CH3F surrounded by one to six water molecules. For systems of similar topologies, CH3F formed hydrogen bonds of nearly the same strength as water. Although CH3F can bind to a second water cluster with only a modest loss in binding energy, it must bind to these clusters as a double hydrogen bond acceptor. This means that CH3F cannot form a low-energy cyclic 2D hydrogen bonding network with water molecules, which limits its solubility in bulk water. However, CH3F should be able to bind to the periphery of small hydrogen bonding networks. These conclusions were not appreciably altered by SMD calculations. A more complete consideration of solvation, especially entropic effects, was not undertaken. Data for geometries, population changes, and vibrational frequency shifts were also analyzed and compared to binding energies.
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IJS, KILJ, NUK, PNG, UL, UM
Cooperativity between intermolecular and intramolecular hydrogen bonds is an important factor determining the strength of donor‐acceptor complexes. Its impact in poly‐1,2‐diols, notably ...polyhydroxybenzenes, is subject to debate. Density functional theory calculations have been performed on complexes of phenol, catechol, pyrogallol and 1,2,3,4‐tetrahydroxybenzene with pyridine, trimethylamine and trimethylphosphine oxide. Binding energies, proton NMR shifts, Quantum Theory of Atoms in Molecules analysis and Interacting Quantum Atoms (IQA) interaction energies reveal a positive cooperative effect of a topological intramolecular hydrogen bond (IMHB) in catechol relative to phenol, with insignificant or small negative effects of further HO groups. Except for catechol complexes, there are no topological IMHBs in any donors or their complexes, although all show Non‐Covalent Interaction isosurfaces. The absence of a topological IMBH in catechol itself is explained by electron density contour plots. Complexes of Me3N and Me3PO with catechol, pyrogallol and 1,2,3,4‐tetrahydroxybenzene display additional intermolecular hydrogen bonds, C‐H…H‐C and C‐H…O=P, respectively, with the hydrogen atom ortho to the bound HO group. The predominantly covalent or electrostatic character of the various hydrogen bond types is discussed in terms of the IQA energy partition scheme, which is also useful for characterising IMHBs in the absence of a bond critical point. These results further our understanding of the nature and the limits of cooperative hydrogen bonding in donor‐acceptor complexes.
Computed binding energies, proton NMR shifts, interaction energies and topological electron density analysis for complexes of phenol, catechol, pyrogallol and 1,2,3,4‐tetrahydroxybenzene with pyridine, trimethylamine and trimethylphosphine oxide reveal significant variations in the hydrogen bond cooperative effect. Trimethylamine complexes show two weak hydrogen‐hydrogen bonds (CC‐H…H‐CN) between methyl group hydrogens and the hydrogen atom ortho to the bound HO group, and the corresponding trimethylphosphine oxide complexes have 10‐fold stronger hydrogen bonds between the phosphorus‐bound oxygen and the same ortho‐hydrogen (CC‐H…O=P).
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BFBNIB, FZAB, GIS, IJS, IZUM, KILJ, NLZOH, NUK, OILJ, PILJ, PNG, SAZU, SBCE, SBMB, UL, UM, UPUK
5.
Does Fluoromethane Form a Hydrogen Bond with Water? Rosenberg, Robert E
The journal of physical chemistry. A, Molecules, spectroscopy, kinetics, environment, & general theory,
11/2012, Volume:
116, Issue:
44
Journal Article
Peer reviewed
Fluorinated organic compounds have become increasingly important in the pharmaceutical and agricultural industries. However, even the simplest aspects of these compounds are still not well ...understood. For instance, it is an open question as to whether fluoroorganics can form a hydrogen bond. To answer this question, this work compares the complex CH3F···HOH with 10 other complexes including the water dimer, the water–ammonia dimer, the methane–water dimer, and the methane dimer, among others. The features that are compared include binding energy and its electrostatic and dispersive components, geometry, vibrational frequencies, charge transfer, and topological analysis of the electron density. All of these are consistent with a hydrogen bond forming in CH3F···HOH. Moreover, all features of this dimer appear to be quite similar in kind, although slightly lesser in degree, than the corresponding features of the water dimer.
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NASA's Orbiting Carbon Observatory-3 (OCO-3) was installed on the International Space Station (ISS) on 10 May 2019. OCO-3 combines the flight spare spectrometer from the Orbiting Carbon Observatory-2 ...(OCO-2) mission, which has been in operation since 2014, with a new Pointing Mirror Assembly (PMA) that facilitates observations of non-nadir targets from the nadir-oriented ISS platform. The PMA is a new feature of OCO-3, which is being used to collect data in all science modes, including nadir (ND), sun-glint (GL), target (TG), and the new snapshot area mapping (SAM) mode.
This work provides an initial assessment of the OCO-3 instrument and algorithm performance, highlighting results from the first 8 months of operations spanning August 2019 through March 2020. During the In-Orbit Checkout (IOC) phase, critical systems such as power and cooling were verified, after which the OCO-3 spectrometer and PMA were subjected to a series of rigorous tests. First light of the OCO-3 spectrometer was on 26 June 2019, with full science operations beginning on 6 August 2019. The OCO-3 spectrometer on-orbit performance is consistent with that seen during preflight testing. Signal to noise ratios are in the expected range needed for high quality retrievals of the column-averaged carbon dioxide (CO2) dry-air mole fraction (XCO2) and solar-induced chlorophyll fluorescence (SIF), which will be used to help quantify and constrain the global carbon cycle.
The first public release of OCO-3 Level 2 (L2) data products, called “vEarly”, is being distributed by NASA's Goddard Earth Sciences Data and Information Services Center (GES DISC). The intent of the vEarly product is to evaluate early mission performance, facilitate comparisons with OCO-2 products, and identify key areas to improve for the next data release. The vEarly XCO2 exhibits a root-mean-squared-error (RMSE) of ≃ 1, 1, 2 ppm versus a truth proxy for nadir-land, TG&SAM, and glint-water observations, respectively. The vEarly SIF shows a correlation with OCO-2 measurements of >0.9 for highly coincident soundings. Overall, the Level 2 SIF and XCO2 products look very promising, with performance comparable to OCO-2. A follow-on version of the OCO-3 L2 product containing a number of refinements, e.g., instrument calibration, pointing accuracy, and retrieval algorithm tuning, is anticipated by early in 2021.
•Orbiting Carbon Observatory-3 has been installed on the International Space Station.•OCO-3 passed in-orbit checkout and began collecting science data August 2019.•The planned mission lifetime of OCO-3 is 3 years; August 2019 to August 2022.•OCO measures total column carbon dioxide and solar induced chlorophyll fluorescence.•The first data product release, vEarly, is publicly available on the NASA DISC.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Complexes of three aromatic diols, catechol, naphthalene‐1,8‐diol, and fluorene‐4,5‐diol, with a series of hydrogen bond acceptors (HBAs) that have oxygen, nitrogen, and sulfur acceptor atoms, have ...been studied by density functional theory (DFT) at the B3LYP/6‐311+G(d,p) level. Binding energies, geometries, infrared spectroscopic (IR) frequencies, nuclear magnetic resonance (NMR) shifts, and measures of the electron density distribution from the Quantum Theory of Atoms in Molecules (QTAIM) are evaluated and compared with data for the corresponding monohydroxy compounds (monols), phenol, naphth‐1‐ol, and fluorene‐4‐ol, in order to assess the importance of cooperativity between intramolecular and intermolecular hydrogen bonding. All measures for all complexes show positive cooperativity whereby both the intermolecular and intramolecular hydrogen bonds are strengthened upon complexation. Cooperativity is weak for catechol and strong for the other two diols and, for all diols, increases with the hydrogen bond basicity of the acceptor. Correlations of IR and NMR metrics against binding energies for a single HBA and all six monols and diols are excellent, but attempts to correlate the same metrics for all HBAs and a single donor are frustrated by differences in intermolecular hydrogen bonding, depending notably on the identity of the acceptor atom in the HBA. Atom–atom interaction energies, calculated by the Interacting Quantum Atoms approach, are used to discuss the covalency of both types of hydrogen bond.
Complexes of catechol, naphthalene‐1,8‐diol, and fluorene‐4,5‐diol with a series of hydrogen bond acceptors show positive cooperativity relative to those of the corresponding monols, both the intermolecular and the intramolecular hydrogen bonds of the diols being strengthened upon complexation. This conclusion is supported by analysis of binding energies, geometries, IR frequencies, proton NMR shifts, QTAIM metrics, and IQA interaction energies. Although cooperativity is weaker for catechol, all diols show that cooperativity increases with the strength of the acceptor.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SBCE, SBMB, UL, UM, UPUK
The role of a defunctioning stoma in patients undergoing low anterior resection for rectal cancer is still the subject of controversy. Recent studies suggest reduced morbidity after low anterior ...rectal resection with a defunctioning stoma.
Retrospective and prospective studies published between 1966 and 2007 were systematically reviewed. Randomized controlled trials (RCTs) comparing anterior resections with or without defunctioning stoma were included in a meta-analysis. The pooled estimates of clinically relevant anastomotic leakages and of reoperations were analyzed using a random effects model (odds ratio and 95% confidence interval, CI).
Relevant retrospective single (n = 18) and multicenter (n = 9) studies were identified and included in the systematic review. Analysis of incoherent data of the leakage rates in these nonrandomized studies demonstrated that a defunctioning stoma did not influence the occurrence of anastomotic failure but seemed to ameliorate the consequences of the leak. Four RCTs were included in the meta-analysis. The odds ratio for clinically relevant anastomotic leakage was 0.32 (95% CI 0.17-0.59), revealing a statistically significant benefit conferred through a defunctioning stoma (Z = 3.65, P = 0.0003). The odds ratio for reoperation because of leakage-caused complications was 0.27 (95% CI 0.14-0.51), with significantly fewer reoperations in patients with a defunctioning stoma (Z = 3.95, P < 0.0001). Overall mortality rates were comparable regardless of the presence of a defunctioning stoma.
A defunctioning stoma reduces the rate of clinically relevant anastomotic leakages and is thus recommended in surgery for low rectal cancers.
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