Internal dynamics of cyclohexanol and the cyclohexanol–water adduct

2019 ◽  
Vol 21 (7) ◽  
pp. 3676-3682 ◽  
Author(s):  
Marcos Juanes ◽  
Weixing Li ◽  
Lorenzo Spada ◽  
Luca Evangelisti ◽  
Alberto Lesarri ◽  
...  
Keyword(s):  
Water Molecule ◽  
Water Dimer ◽  
Hydroxyl Group ◽  
Rotational Spectrum ◽  
Internal Dynamics

Two for a tango: the rotational spectrum of a cyclohexanol–water dimer evidences a concerted motion of the water molecule and the hydroxyl group of the ring.

scholarly journals Density functional theory meta GGA study of water adsorption in MIL-53(Cr)

2019 ◽  
Vol 34 (3) ◽  
pp. 227-232 ◽  
Author(s):  
E. Cockayne
Keyword(s):  
Density Functional Theory ◽  
Water Molecule ◽  
Density Functional ◽  
Critical Concentration ◽  
Metal Organic Framework ◽  
Water Dimer ◽  
Hydroxyl Group ◽  
Water Molecules ◽  
Generalized Gradient ◽  
Functional Theory

We use density functional theory meta-generalized gradient approximation TPSS + D3(BJ) + U + J calculations to investigate the energetics and geometry of water molecules in the flexible metal-organic framework material Materials of Institut Lavoisier (MIL)-53(Cr) as a function of cell volume. The critical concentration of water to cause the transition from the large pore (lp) to the narrow pore (np) structure is estimated to be about 0.13 water molecule per Cr. At a concentration x = 1 water molecule per Cr, the zero-temperature np and lp configurations each have a hydrogen bond between the H of each framework hydroxyl group and water oxygen (OW). At intermediate volumes, water dimer-like configurations are observed. A concentration x = 1.25 leads to hydrogen bonding between water molecules in the np phase that is absent for x = 1. Our results suggest possible mechanisms for pore closing in hydrated MIL-53(Cr).

The pKa value of the proximal water molecule trans to a high-valent MnVO porphyrin: towards the control of reactivity by pH

2017 ◽  
Vol 46 (36) ◽  
pp. 12088-12094 ◽  
Author(s):  
Laurie Saint-Germes ◽  
Laure Bar ◽  
Jérôme Dejeu ◽  
Nicolas Spinelli ◽  
Eric Defrancq ◽  
...  
Keyword(s):  
Water Molecule ◽  
Hydroxyl Group ◽  
Protonation State ◽  
Pka Value ◽  
High Valent

In water, the protonation state of the proximal water molecule of a high-valent manganese-oxo porphyrin could be controlled by pH. While in interaction with DNA the porphyrin was able to cleave DNA, only when the proximal water molecule was in the form of a hydroxyl group.

scholarly journals Rotational spectra of tetracyclic quinolizidine alkaloids: does a water molecule flip sparteine?

2017 ◽  
Vol 19 (27) ◽  
pp. 17553-17559 ◽  
Author(s):  
Alberto Lesarri ◽  
Ruth Pinacho ◽  
Lourdes Enríquez ◽  
José E. Rubio ◽  
Martín Jaraíz ◽  
...  
Keyword(s):  
Water Molecule ◽  
Water Dimer ◽  
Quinolizidine Alkaloids ◽  
Parent Molecule ◽  
Rotational Spectra

Flipping or not flipping? The sparteine–water dimer generated in a jet expansion retains the trans conformation of the parent molecule.

scholarly journals The transition state for peptide bond formation reveals the ribosome as a water trap

2010 ◽  
Vol 107 (5) ◽  
pp. 1888-1893 ◽  
Author(s):  
Göran Wallin ◽  
Johan Åqvist
Keyword(s):  
Water Molecule ◽  
Transition State ◽  
Activation Enthalpy ◽  
Molecular Model ◽  
Isotope Effects ◽  
Bond Formation ◽  
Transition States ◽  
Peptide Bond ◽  
Hydroxyl Group ◽  
Peptide Bond Formation

Recent progress in elucidating the peptide bond formation process on the ribosome has led to notion of a proton shuttle mechanism where the 2'-hydroxyl group of the P-site tRNA plays a key role in mediating proton transfer between the nucleophile and leaving group, whereas ribosomal groups do not actively participate in the reaction. Despite these advances, the detailed nature of the transition state for peptidyl transfer and the role of several trapped water molecules in the peptidyl transferase center remain major open questions. Here, we employ high-level quantum chemical ab initio calculations to locate and characterize global transition states for the reaction, described by a molecular model encompassing all the key elements of the reaction center. The calculated activation enthalpy as well as structures are in excellent agreement with experimental data and point to feasibility of an eight-membered “double proton shuttle” mechanism in which an auxiliary water molecule, observed both in computer simulations and crystal structures, actively participates. A second conserved water molecule is found to be of key importance for stabilizing developing negative charge on the substrate oxyanion and its presence is catalytically favorable both in terms of activation enthalpy and entropy. Transition states calculated both for six- and eight-membered mechanisms are invariably late and do not involve significant charge development on the attacking amino group. Predicted kinetic isotope effects consistent with this picture are similar to those observed for uncatalyzed ester aminolysis reactions in solution.

Rotational Spectrum and Internal Dynamics of Methylpyruvate

2013 ◽  
Vol 117 (3) ◽  
pp. 590-593 ◽  
Author(s):  
Biagio Velino ◽  
Laura B. Favero ◽  
Paolo Ottaviani ◽  
Assimo Maris ◽  
Walther Caminati
Keyword(s):  
Rotational Spectrum ◽  
Internal Dynamics

Chalcogen bond and internal dynamics of the 2,2,4,4-tetrafluoro-1,3-dithietane⋯water complex

2019 ◽  
Vol 21 (28) ◽  
pp. 15656-15661 ◽  
Author(s):  
Yan Jin ◽  
Xiaolong Li ◽  
Qian Gou ◽  
Gang Feng ◽  
Jens-Uwe Grabow ◽  
...  
Keyword(s):  
High Resolution ◽  
Rotational Spectroscopy ◽  
Rotational Spectrum ◽  
Internal Dynamics ◽  
Chalcogen Bond ◽  
Water Complex

The rotational spectrum of the 2,2,4,4-tetrafluoro-1,3-dithietane⋯water complex has been investigated by high resolution rotational spectroscopy. Inversion of the water around its C2 axis is hindered by a barrier determined to be 87.4(2) cm−1.

THE STRUCTURAL BASIS OF FERROELECTRICITY IN COLEMANITE

1966 ◽  
Vol 44 (12) ◽  
pp. 3083-3107 ◽  
Author(s):  
F. N. Hainsworth ◽  
H. E. Petch
Keyword(s):  
Neutron Diffraction ◽  
Water Molecule ◽  
Ferroelectric Phase ◽  
The Other ◽  
Hydroxyl Group ◽  
Structural Basis ◽  
Hydrogen Atoms ◽  
Complete Structure ◽  
Ferroelectric State ◽  
Order Of Magnitude

The complete structure of colemanite, CaB3O4(OH)3∙H2O, in both its nonpolar and ferroelectric phases, has been determined by neutron diffraction. This work shows that one of the hydrogen atoms of the water molecule and the hydrogen of an adjacent hydroxyl group, which are in a state of dynamic disorder in the nonpolar phase, settle into ordered noncentric positions in the ferroelectric phase. The ordering of the hydrogen atoms is accompanied by small displacements of the other atoms from the positions they occupy in the nonpolar phase. Assuming reasonable charge assignments, the magnitude of the spontaneous polarization calculated from the observed positional changes is of the same order of magnitude as the experimental value. On the basis of these results, a model for the atomistic mechanism of the transition to the ferroelectric state is advanced.

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