Homoselenocysteine — An oxygen or selenium acid in the gas phase?

2010 ◽  
Vol 88 (8) ◽  
pp. 744-753 ◽  
Author(s):  
Marcela Hurtado ◽  
Otilia Mó ◽  
Manuel Yáñez
Keyword(s):  
Gas Phase ◽  
Global Minimum ◽  
Group Structure ◽  
Hydroxyl Group ◽  
Amino Group ◽  
Deprotonated Form ◽  
Protonated Amino Group ◽  
Stability Order ◽  
The Stability ◽  
Intramolecular Hydrogen

The potential energy surface of l-homoselenocysteine (HSEC) has been explored through the use of B3LYP/6-311+G(d,p) calculations. In this survey, seventy-seven different conformers have been located. These local minima can be classified in four groups, A–D. Structures A, B, and D are stabilized by intramolecular hydrogen bonds (IMHBs) with the amino group acting as the hydrogen bond (HB) donor and the carbonyl group (structures A and D) or the hydroxyl group (structure B) as HB acceptors. The structures in set C present an IMHB with the amino group acting as the HB acceptor and the hydroxyl group as the HB donor. The stability order decreases in the following order: A > B > C > D. From their relative stabilities it can be concluded that only three of these conformers, namely A1, A4, and A5, would exist in the gas phase at room temperature. The most stable deprotonated form corresponds to a Se-deprotated species stabilized by a strong IMHB between the hydroxyl group and the Se atom. However, a direct deprotonation of the most stable neutrals lead to O-deprotonated species, which eventually isomerize to yield the global minimum. Hence, we can conclude that, quite unexpectedly, HSEC behaves as a Se acid in the gas phase, its intrinsic acidity being 1374 kJ mol–1 at the B3LYP/6-311++G(3df,2p) level of theory. The most stable protonated forms are systematically the N-protonated ones, the global minimum being a structure stabilized through an IMHB involving the protonated amino group as the HB donor and the SeH group as the HB acceptor. The calculated gas-phase proton affinity (PA) at the B3LYP/6-311++G(3df,2p) level of theory is 930 kJ mol–1.

scholarly journals Influence of catecholic ring torsion on hydroxyflavones

2020 ◽  
Vol 13 (1) ◽  
pp. 49-55
Author(s):  
Martin Michalík ◽  
Monika Biela ◽  
Denisa Cagardová ◽  
Vladimír Lukeš
Keyword(s):  
Gas Phase ◽  
Phenyl Ring ◽  
Density Functional ◽  
Hydroxyl Group ◽  
Torsional Deformation ◽  
Functional Theory ◽  
Electron Transitions ◽  
The Density Functional Theory ◽  
Intramolecular Hydrogen ◽  
Theoretical Results

AbstractSystematic quantum chemical investigation of quercetin and selected eight mono- and bihydroxyflavonols is presented. Structural analysis based on the Density Functional Theory showed that the energetically preferred conformation of flavonols substituted at the C5 and C3 atoms by a hydroxyl group is stabilised via intramolecular hydrogen bonds occurring between the (C4)O···HO(3 or 5) atomic pairs. Depending on the hydroxyl group positions, energetically preferred torsional orientation of the phenyl ring with respect to the planar benzo-γ-pyrone moiety changed from 0 to 180 degrees. Gas-phase electron transitions were investigated using the time-dependent DFT treatment. The dependence of maximal wavelengths on the torsional deformation of the phenyl ring is of a similar shape, i.e. minima observed for the perpendicular orientation and maxima for the planar one. Shape and energies of the Highest Occupied (HOMO) and Lowest Unoccupied (LUMO) Molecular Orbitals were compared. The obtained theoretical results were compared with available experimental data.

DFT STUDY ON CONFORMATIONAL BEHAVIOR OF HYDROGEN ION ABSTRACTIONS OF CYTOSINE NUCLEOSIDES: AIM AND NBO ANALYSIS

2011 ◽  
Vol 10 (06) ◽  
pp. 803-817 ◽  
Author(s):  
ZAHRA ALIAKBAR TEHRANI ◽  
ALIREZA FATTAHI ◽  
MARJAN JEBELI JAVAN ◽  
MOHAMMAD MAHMOODI HASHEMI
Keyword(s):  
Structural Parameters ◽  
Nbo Analysis ◽  
Basis Sets ◽  
Orbital Method ◽  
Acceptor Interaction ◽  
Hydride Ion ◽  
Stability Order ◽  
The Stability ◽  
Intramolecular Hydrogen ◽  
Hydride Ions

In this paper, we explore theoretically energetic and structural properties of the possible cations formed via hydride ion abstraction at various sites of sugar part of cytosine nucleosides by employing B3LYP exchange-correlation functional with 6-311++G (d,p) orbital basis sets. In general, the hydride ion abstracted sugar cations of cytosine nucleosides have the following stability sequence: caH2′ > caH1′ > caH3′ > caH4′ > caH5′ for cytidine and caH1′ > caH4′ > caH3′ > caH5′ > caH2′ for deoxycytidine. Furthermore, the effect of solvent environment on the stability order of cations integral equation formalism of the polarized model (IEF-PCM) was employed to model aqueous solution. The natural bond orbital method was used for quantitative analysis of the electron delocalization donor–acceptor interaction of various hydride ions abstracted centers of cytosine nucleosides. The role of CH⋯O and HO⋯H intramolecular hydrogen bonds in the stability of cations is investigated based on the results of topological properties of atom in molecule theory. Moreover, variations of significant structural parameters such as puckering amplitudes and phase angles of sugar parts of cytosine nucleosides after cation formation are also found.

The role of aromatic rings as hydrogen-bond acceptors in molecular recognition

1993 ◽  
Vol 345 (1674) ◽  
pp. 105-112 ◽  
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Gas Phase ◽  
Signal Transmission ◽  
Aromatic Rings ◽  
Aromatic Interactions ◽  
Proton Donors ◽  
The Stability ◽  
Intramolecular Hydrogen

Observations of phenol-benzene and ammonia—benzene complexes in the gas phase show that hydrogen bonds link their proton donors to the π electrons of the benzene with a bond energy of between 2 and 4 kcal mol -1 , large enough to be biologically significant. Intramolecular hydrogen bonds between OH and NH donors and aromatic acceptors have also been found in crystal structures of organic compounds. NH-aromatic interactions stabilize x-helices if donors and acceptors occur at successive turns of the helix. These interactions also contribute to the stability of several proteins and play an important part in cellular and synaptic signal transmission.

Stability, polarity, intramolecular interactions and π-electron delocalization for all eighteen tautomers rotamers of uracil. DFT studies in the gas phase

2009 ◽  
Vol 74 (1) ◽  
pp. 57-72 ◽  
Author(s):  
Ewa D. Raczyńska ◽  
Katarzyna Zientara ◽  
Tomasz M. Stępniewski ◽  
Katarzyna Kolczyńska
Keyword(s):  
Gas Phase ◽  
Functional Groups ◽  
Intramolecular Interactions ◽  
Electron Delocalization ◽  
Dft Studies ◽  
Tautomeric Equilibria ◽  
Aromatic Character ◽  
Stability Order ◽  
The Stability ◽  
Main Factor

Complete tautomeric equilibria were investigated for uracil at the DFT(B3LYP)/6-311+G(d,p) level to establish the stability order of all possible 18 tautomers-rotamers in the gas phase and to characterize their internal effects, polarity and aromatic character. Although the di-NH form strongly predominates (100%) in the mixture, the NH–OH, di-OH and CH–NH forms can be also considered. The favored tautomer is moderately stabilized by intramolecular interactions (attractions of the NH and C=O groups); it is also moderately polar and moderately delocalized. Stability of the functional groups (both amide functions) seems to be more important than intramolecular interactions, polarity and aromaticity. This is probably the main factor that dictates the tautomeric preferences in the uracil molecule.

scholarly journals Perturbating Intramolecular Hydrogen Bonds through Substituent Effects or Non-Covalent Interactions

Molecules ◽  
2021 ◽  
Vol 26 (12) ◽  
pp. 3556
Author(s):  
Al Mokhtar Lamsabhi ◽  
Otilia Mó ◽  
Manuel Yáñez
Keyword(s):  
Hydrogen Bonds ◽  
Substituent Effects ◽  
Amino Alcohols ◽  
Nbo Analysis ◽  
Hydroxyl Group ◽  
Amino Group ◽  
Isodesmic Reactions ◽  
Intramolecular Hydrogen Bonds ◽  
Covalent Interaction ◽  
Intramolecular Hydrogen

An analysis of the effects induced by F, Cl, and Br-substituents at the α-position of both, the hydroxyl or the amino group for a series of amino-alcohols, HOCH2(CH2)nCH2NH2 (n = 0–5) on the strength and characteristics of their OH···N or NH···O intramolecular hydrogen bonds (IMHBs) was carried out through the use of high-level G4 ab initio calculations. For the parent unsubstituted amino-alcohols, it is found that the strength of the OH···N IMHB goes through a maximum for n = 2, as revealed by the use of appropriate isodesmic reactions, natural bond orbital (NBO) analysis and atoms in molecules (AIM), and non-covalent interaction (NCI) procedures. The corresponding infrared (IR) spectra also reflect the same trends. When the α-position to the hydroxyl group is substituted by halogen atoms, the OH···N IMHB significantly reinforces following the trend H < F < Cl < Br. Conversely, when the substitution takes place at the α-position with respect to the amino group, the result is a weakening of the OH···N IMHB. A totally different scenario is found when the amino-alcohols HOCH2(CH2)nCH2NH2 (n = 0–3) interact with BeF2. Although the presence of the beryllium derivative dramatically increases the strength of the IMHBs, the possibility for the beryllium atom to interact simultaneously with the O and the N atoms of the amino-alcohol leads to the global minimum of the potential energy surface, with the result that the IMHBs are replaced by two beryllium bonds.

2-Deoxyribose Radicals in the Gas Phase and Aqueous Solution. Transient Intermediates of Hydrogen Atom Abstraction from 2-Deoxyribofuranose

2005 ◽  
Vol 70 (11) ◽  
pp. 1769-1786 ◽  
Author(s):  
Luc A. Vannier ◽  
Chunxiang Yao ◽  
František Tureček
Keyword(s):  
Aqueous Solution ◽  
Hydrogen Atom ◽  
Gas Phase ◽  
Computational Study ◽  
Hydrogen Atom Abstraction ◽  
Oh Radical ◽  
Free Energies ◽  
Intramolecular Hydrogen ◽  
Solvation Free Energies ◽  
Transient Intermediates

A computational study at correlated levels of theory is reported to address the structures and energetics of transient radicals produced by hydrogen atom abstraction from C-1, C-2, C-3, C-4, C-5, O-1, O-3, and O-5 positions in 2-deoxyribofuranose in the gas phase and in aqueous solution. In general, the carbon-centered radicals are found to be thermodynamically and kinetically more stable than the oxygen-centered ones. The most stable gas-phase radical, 2-deoxyribofuranos-5-yl (5), is produced by H-atom abstraction from C-5 and stabilized by an intramolecular hydrogen bond between the O-5 hydroxy group and O-1. The order of radical stabilities is altered in aqueous solution due to different solvation free energies. These prefer conformers that lack intramolecular hydrogen bonds and expose O-H bonds to the solvent. Carbon-centered deoxyribose radicals can undergo competitive dissociations by loss of H atoms, OH radical, or by ring cleavages that all require threshold dissociation or transition state energies >100 kJ mol-1. This points to largely non-specific dissociations of 2-deoxyribose radicals when produced by exothermic hydrogen atom abstraction from the saccharide molecule. Oxygen-centered 2-deoxyribose radicals show only marginal thermodynamic and kinetic stability and are expected to readily fragment upon formation.

scholarly journals Crystal structure of atazanavir, C38H52N6O7

2020 ◽  
Vol 35 (2) ◽  
pp. 129-135
Author(s):  
James A. Kaduk ◽  
Amy M. Gindhart ◽  
Thomas N. Blanton
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Powder Diffraction ◽  
Density Functional ◽  
Carbonyl Oxygen ◽  
Hydroxyl Group ◽  
Amide Nitrogen ◽  
Classical Hydrogen Bond ◽  
Intramolecular Hydrogen ◽  
Atazanavir Sulfate

The crystal structure of atazanavir has been solved and refined using synchrotron X-ray powder diffraction data and optimized using density functional techniques. Atazanavir crystallizes in space group P21 (#4) with a = 15.33545(7), b = 5.90396(3), c = 21.56949(13) Å, β = 96.2923(4)°, V = 1941.134(11) Å3, and Z = 2. Despite being labeled as “atazanavir sulfate”, the commercial reagent sample consisted of atazanavir free base. The structure consists of an array of extended-conformation molecules parallel to the ac-plane. Although the atazanavir molecule contains only four classical hydrogen bond donors, hydrogen bonding is, surprisingly, important to the crystal energy. Both intra- and intermolecular hydrogen bonds are significant. The hydroxyl group forms bifurcated intramolecular hydrogen bonds to a carbonyl oxygen atom and an amide nitrogen. Several amide nitrogens act as donors to the hydroxyl group and carbonyl oxygen atoms. An amide nitrogen acts as a donor to another amide nitrogen. Several methyl, methylene, methyne, and phenyl hydrogens participate in hydrogen bonds to carbonyl oxygens, an amide nitrogen, and the pyridine nitrogen. The powder pattern is included in the Powder Diffraction File™ as entry 00-065-1426.

Serine–Ca2+ versus serine–Cu2+ complexes — A theoretical perspective

2010 ◽  
Vol 88 (8) ◽  
pp. 759-768 ◽  
Author(s):  
Al Mokhtar Lamsabhi ◽  
Otilia Mó ◽  
Manuel Yáñez
Keyword(s):  
Gas Phase ◽  
Electron Density ◽  
Potential Energy Surfaces ◽  
Metal Ion ◽  
Theoretical Perspective ◽  
Binding Energies ◽  
Interacting Systems ◽  
Intramolecular Hydrogen ◽  
Energy Surfaces ◽  
Doubly Charged

The association of Ca2+ and Cu2+ to serine was investigated by means of B3LYP DFT calculations. The [serine–M]2+ (M = Ca, Cu) potential energy surfaces include, as does the neutral serine, a large number of conformers, in which a drastic reorganization of the electron density of the serine moiety is observed. This leads to significant changes in the number and strength of the intramolecular hydrogen bonds existing in the neutral serine tautomers. In some cases, a proton is transferred from the carboxylic OH group to the amino group and accordingly, some of the more stable [serine–M]2+ complexes can be viewed as the result of the interaction of the zwiterionic form of serine with the doubly charged metal ion. Whereas the interaction between Ca2+ and serine is essentially electrostatic, that between Cu2+ and serine has a non-negligible covalent character, reflected in larger electron densities at the bond critical points between the metal and the base, in the negative values of the electron density between the two interacting systems, and in much larger Cu2+ than Ca2+ binding energies. More importantly, the interaction with Cu2+ is followed by a partial oxidation of the base, which is not observed when the metal ion is Ca2+. The main consequence is that in Cu2+ complexes a significant acidity enhancement of the serine moiety takes place, which strongly favors the deprotonation of the [serine–Cu]2+ complexes. This is not the case for Ca2+ complexes. Thus, [serine–Ca]2+ complexes, like those formed by urea, thiourea, selenourea, or glycine, should be detected in the gas phase. Conversely, the complexes with Cu2+ should deprotonate spontaneously and therefore only [(serine–H)–Cu]+ monocations should be experimentally accessible.

scholarly journals Molecular Properties of Bare and Microhydrated Vitamin B5–Calcium Complexes

2021 ◽  
Vol 22 (2) ◽  
pp. 692
Author(s):  
Davide Corinti ◽  
Barbara Chiavarino ◽  
Debora Scuderi ◽  
Caterina Fraschetti ◽  
Antonello Filippi ◽  
...  
Keyword(s):  
Gas Phase ◽  
Pantothenic Acid ◽  
Isomeric Form ◽  
Deprotonated Form ◽  
Linear Absorption ◽  
Vitamin B5 ◽  
Essential Nutrient ◽  
Calcium Complexes ◽  
Singly Charged ◽  
Phase Population

Pantothenic acid, also called vitamin B5, is an essential nutrient involved in several metabolic pathways. It shows a characteristic preference for interacting with Ca(II) ions, which are abundant in the extracellular media and act as secondary mediators in the activation of numerous biological functions. The bare deprotonated form of pantothenic acid, [panto-H]−, its complex with Ca(II) ion, [Ca(panto-H)]+, and singly charged micro-hydrated calcium pantothenate [Ca(panto-H)(H2O)]+ adduct have been obtained in the gas phase by electrospray ionization and assayed by mass spectrometry and IR multiple photon dissociation spectroscopy in the fingerprint spectral range. Quantum chemical calculations at the B3LYP(-D3) and MP2 levels of theory were performed to simulate geometries, thermochemical data, and linear absorption spectra of low-lying isomers, allowing us to assign the experimental absorptions to particular structural motifs. Pantothenate was found to exist in the gas phase as a single isomeric form showing deprotonation on the carboxylic moiety. On the contrary, free and monohydrated calcium complexes of deprotonated pantothenic acid both present at least two isomers participating in the gas-phase population, sharing the deprotonation of pantothenate on the carboxylic group and either a fourfold or fivefold coordination with calcium, thus justifying the strong affinity of pantothenate for the metal.

The influence of the chlorine-hydrogen ratio in the gas phase on the stability of the {113} faces of silicon in Si-H-Cl CVD

1990 ◽  
Vol 102 (1-2) ◽  
pp. 233-244 ◽  
Author(s):  
J.G.E. Gardeniers ◽  
M.M.W. Mooren ◽  
M.H.J.M. De Croon ◽  
L.J. Giling
Keyword(s):  
Gas Phase ◽  
The Stability
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