scholarly journals Understanding the Exceptional Properties of Nitroacetamides in Water: A Computational Model Including the Solvent

Molecules ◽  
2018 ◽  
Vol 23 (12) ◽  
pp. 3308 ◽  
Author(s):  
Giovanni La Penna ◽  
Fabrizio Machetti
Keyword(s):  
Proton Transfer ◽  
Density Functional ◽  
Water Environment ◽  
Average Energy ◽  
Thermal Fluctuations ◽  
Energy Difference ◽  
Tautomeric Forms ◽  
Geminal Proton ◽  
Solvent Molecules ◽  
Explicit Water

Proton transfer in water involving C–H bonds is a challenge and nitro compounds have been studied for many years as good examples. The effect of substituents on acidity of protons geminal to the nitro group is exploited here with new p K a measurements and electronic structure models, the latter including explicit water environment. Substituents with the amide moiety display an exceptional combination of acidity and solubility in water. In order to find a rationale for the unexpected p K a changes in the (ZZ ′ )NCO- substituents, we measured and modeled the p K a with Z=Z ′ =H and Z=Z ′ =methyl. The dominant contribution to the observed p K a can be understood with advanced computational experiments, where the geminal proton is smoothly moved to the solvent bath. These models, mostly based on density-functional theory (DFT), include the explicit solvent (water) and statistical thermal fluctuations. As a first approximation, the change of p K a can be correlated with the average energy difference between the two tautomeric forms (aci and nitro, respectively). The contribution of the solvent molecules interacting with the solute to the proton transfer mechanism is made evident.

A New Interpretation of the Structure and Solvent Dependence of the Far UV Circular Dichroism Spectrum of Short Oligopeptides

2019 ◽  
Author(s):  
Anshuman Kumar ◽  
Reinhard Schweitzer-Stenner ◽  
Bryan Wong
Keyword(s):  
Density Functional ◽  
Density Functional Theory Calculations ◽  
Cd Spectra ◽  
Functional Theory ◽  
Polyproline Ii ◽  
Solvent Dependence ◽  
Explicit Consideration ◽  
New Interpretation ◽  
Implicit And Explicit ◽  
Explicit Water

In this work, we carry out new time-dependent density functional theory calculations on the cationic tripeptide GAG in implicit and explicit water to determine the transitions that give rise to the observed CD signals of polyproline II and β-strand conformations. Our results reveal a plethora of electronic transitions that are governed by configurational interactions between multiple molecular orbital transitions of comparable energy. We also show that reproducing the CD spectra of polyproline II and β-strand conformations requires the explicit consideration of water molecules. The structure dependence of delocalized occupied orbitals contributes to the experimentally-observed invalidation of Flory’s isolated pair hypothesis.

A New Interpretation of the Structure and Solvent Dependence of the Far UV Circular Dichroism Spectrum of Short Oligopeptides

2019 ◽  
Author(s):  
Anshuman Kumar ◽  
Reinhard Schweitzer-Stenner ◽  
Bryan Wong
Keyword(s):  
Density Functional ◽  
Density Functional Theory Calculations ◽  
Cd Spectra ◽  
Functional Theory ◽  
Polyproline Ii ◽  
Solvent Dependence ◽  
Explicit Consideration ◽  
New Interpretation ◽  
Implicit And Explicit ◽  
Explicit Water

In this work, we carry out new time-dependent density functional theory calculations on the cationic tripeptide GAG in implicit and explicit water to determine the transitions that give rise to the observed CD signals of polyproline II and β-strand conformations. Our results reveal a plethora of electronic transitions that are governed by configurational interactions between multiple molecular orbital transitions of comparable energy. We also show that reproducing the CD spectra of polyproline II and β-strand conformations requires the explicit consideration of water molecules. The structure dependence of delocalized occupied orbitals contributes to the experimentally-observed invalidation of Flory’s isolated pair hypothesis.

scholarly journals Non-Covalent Forces in Naphthazarin—Cooperativity or Competition in the Light of Theoretical Approaches

2021 ◽  
Vol 22 (15) ◽  
pp. 8033
Author(s):  
Aneta Jezierska ◽  
Kacper Błaziak ◽  
Sebastian Klahm ◽  
Arne Lüchow ◽  
Jarosław J. Panek
Keyword(s):  
Monte Carlo ◽  
Perturbation Theory ◽  
Potential Energy ◽  
Proton Transfer ◽  
Ir Spectra ◽  
Quantum Monte Carlo ◽  
Density Functional ◽  
Theoretical Approaches ◽  
Study Results ◽  
Intramolecular Hydrogen

Non-covalent interactions responsible for molecular features and self-assembly in Naphthazarin C polymorph were investigated on the basis of diverse theoretical approaches: Density Functional Theory (DFT), Diffusion Quantum Monte Carlo (DQMC), Symmetry-Adapted Perturbation Theory (SAPT) and Car-Parrinello Molecular Dynamics (CPMD). The proton reaction paths in the intramolecular hydrogen bridges were studied. Two potential energy minima were found indicating that the proton transfer phenomena occur in the electronic ground state. Diffusion Quantum Monte Carlo (DQMC) and other levels of theory including Coupled Cluster (CC) employment enabled an accurate inspection of Potential Energy Surface (PES) and revealed the energy barrier for the proton transfer. The structure and reactivity evolution associated with the proton transfer were investigated using Harmonic Oscillator Model of Aromaticity - HOMA index, Fukui functions and Atoms In Molecules (AIM) theory. The energy partitioning in the studied dimers was carried out based on Symmetry-Adapted Perturbation Theory (SAPT) indicating that dispersive forces are dominant in the structure stabilization. The CPMD simulations were performed at 60 K and 300 K in vacuo and in the crystalline phase. The temperature influence on the bridged protons dynamics was studied and showed that the proton transfer phenomena were not observed at 60 K, but the frequent events were noticed at 300 K in both studied phases. The spectroscopic signatures derived from the CPMD were computed using Fourier transformation of autocorrelation function of atomic velocity for the whole molecule and bridged protons. The computed gas-phase IR spectra showed two regions with OH absorption that covers frequencies from 2500 cm−1 to 2800 cm−1 at 60 K and from 2350 cm−1 to 3250 cm−1 at 300 K for both bridged protons. In comparison, the solid state computed IR spectra revealed the environmental influence on the vibrational features. For each of them absorption regions were found between 2700–3100 cm−1 and 2400–2850 cm−1 at 60 K and 2300–3300 cm−1 and 2300–3200 cm−1 at 300 K respectively. Therefore, the CPMD study results indicated that there is a cooperation of intramolecular hydrogen bonds in Naphthazarin molecule.

scholarly journals Minimal Optimized Effective Potentials for Density Functional Theory Studies on Excited-State Proton Dissociation

Micromachines ◽  
2021 ◽  
Vol 12 (6) ◽  
pp. 679
Author(s):  
Pouya Partovi-Azar ◽  
Daniel Sebastiani
Keyword(s):  
Density Functional Theory ◽  
Excited State ◽  
Proton Transfer ◽  
Density Functional ◽  
Photochemical Reactions ◽  
Transfer Energy ◽  
Functional Theory ◽  
Effective Potentials ◽  
Proton Dissociation ◽  
Dissociation Curves

Recently, a new method [P. Partovi-Azar and D. Sebastiani, J. Chem. Phys. 152, 064101 (2020)] was proposed to increase the efficiency of proton transfer energy calculations in density functional theory by using the T1 state with additional optimized effective potentials instead of calculations at S1. In this work, we focus on proton transfer from six prototypical photoacids to neighboring water molecules and show that the reference proton dissociation curves obtained at S1 states using time-dependent density functional theory can be reproduced with a reasonable accuracy by performing T1 calculations at density functional theory level with only one additional effective potential for the acidic hydrogens. We also find that the extra effective potentials for the acidic hydrogens neither change the nature of the T1 state nor the structural properties of solvent molecules upon transfer from the acids. The presented method is not only beneficial for theoretical studies on excited state proton transfer, but we believe that it would also be useful for studying other excited state photochemical reactions.

scholarly journals On the Importance of Atomic Fluctuations, Protein Flexibility, and Solvent in Ion Permeation

2004 ◽  
Vol 124 (6) ◽  
pp. 679-690 ◽  
Author(s):  
Toby W. Allen ◽  
O.S. Andersen ◽  
Benoit Roux
Keyword(s):  
Ion Channel ◽  
Protein Function ◽  
Channel Model ◽  
Protein Structures ◽  
Thermal Fluctuations ◽  
Model Parameters ◽  
Ion Permeation ◽  
Model Calculations ◽  
Channel Interactions ◽  
Solvent Molecules

Proteins, including ion channels, often are described in terms of some average structure and pictured as rigid entities immersed in a featureless solvent continuum. This simplified view, which provides for a convenient representation of the protein's overall structure, incurs the risk of deemphasizing important features underlying protein function, such as thermal fluctuations in the atom positions and the discreteness of the solvent molecules. These factors become particularly important in the case of ion movement through narrow pores, where the magnitude of the thermal fluctuations may be comparable to the ion pore atom separations, such that the strength of the ion channel interactions may vary dramatically as a function of the instantaneous configuration of the ion and the surrounding protein and pore water. Descriptions of ion permeation through narrow pores, which employ static protein structures and a macroscopic continuum dielectric solvent, thus face fundamental difficulties. We illustrate this using simple model calculations based on the gramicidin A and KcsA potassium channels, which show that thermal atomic fluctuations lead to energy profiles that vary by tens of kcal/mol. Consequently, within the framework of a rigid pore model, ion-channel energetics is extremely sensitive to the choice of experimental structure and how the space-dependent dielectric constant is assigned. Given these observations, the significance of any description based on a rigid structure appears limited. Creating a conducting channel model from one single structure requires substantial and arbitrary engineering of the model parameters, making it difficult for such approaches to contribute to our understanding of ion permeation at a microscopic level.

scholarly journals Relevance of Hydrogen Bonds for the Histamine H2 Receptor-Ligand Interactions: A Lesson from Deuteration

Biomolecules ◽  
2020 ◽  
Vol 10 (2) ◽  
pp. 196 ◽  
Author(s):  
Mojca Kržan ◽  
Jan Keuschler ◽  
Janez Mavri ◽  
Robert Vianello
Keyword(s):  
Hydrogen Bonding ◽  
Active Sites ◽  
Density Functional ◽  
Receptor Activation ◽  
Histamine H2 Receptor ◽  
Therapeutic Practice ◽  
H2 Receptor ◽  
Ligand Interactions ◽  
Solvent Molecules ◽  
Near Future

We used a combination of density functional theory (DFT) calculations and the implicit quantization of the acidic N–H and O–H bonds to assess the effect of deuteration on the binding of agonists (2-methylhistamine and 4-methylhistamine) and antagonists (cimetidine and famotidine) to the histamine H2 receptor. The results show that deuteration significantly increases the affinity for 4-methylhistamine and reduces it for 2-methylhistamine, while leaving it unchanged for both antagonists, which is found in excellent agreement with experiments. The revealed trends are interpreted in the light of the altered strength of the hydrogen bonding upon deuteration, known as the Ubbelohde effect, which affects ligand interactions with both active sites residues and solvent molecules preceding the binding, thus providing strong evidence for the relevance of hydrogen bonding for this process. In addition, computations further underline an important role of the Tyr250 residue for the binding. The obtained insight is relevant for the therapy in the context of (per)deuterated drugs that are expected to enter therapeutic practice in the near future, while this approach may contribute towards understanding receptor activation and its discrimination between agonists and antagonists.

scholarly journals GGA/PBE study of the spin isomers of Fe34,40, Co23,34, and Co12Cu Clusters with Selected Geometries

2017 ◽  
Vol 56 (3) ◽  
Author(s):  
Faustino Aguilera-Granja ◽  
Andrés Vega ◽  
Luis Carlos Balbás
Keyword(s):  
Ground State ◽  
Density Functional ◽  
Energy Difference ◽  
Many Body ◽  
Generalized Gradient ◽  
Structural Isomers ◽  
Functional Theory ◽  
Ferromagnetic Ground State ◽  
Spin Isomers ◽  
Pseudo Potential

In a recent beam deflecting experiment was found that high and low spin states of pure Fe<sub>n</sub> and Co<sub>n</sub> clusters with <em>n</em> ≤ 300 atoms coexist at cryogenic temperatures. In this work we have studied the high spin (HS) and low spin (LS) states of several structural isomers of Co<sub>23</sub>, Co<sub>34</sub>, Fe<sub>34</sub>, and Fe<sub>40</sub> using the generalized gradient approximation (GGA) to density functional theory as implemented in the first-principles pseudo-potential code SIESTA. The calculated energy difference between these HS and LS isomers is not consistent with the observed coexistence, which can be due to an insufficient account of many body correlation effects in the GGA description, or to unknown isomer structures of these clusters. We have calculated within the same tools the magnetic isomers of Co<sub>12</sub>Cu cluster aimed to re-visit a former DFT prediction of an anti-ferromagnetic ground state. We find, however, a ferromagnetic ground state as expected on physical grounds. Our results exemplify the difficulties of the current DFT approaches to describe the magnetic properties of transition metal systems.

scholarly journals Impact of climatic variability on durum wheat (Triticum durum L.) yields in North Western of Algeria

2016 ◽  
Vol 5 (1) ◽  
pp. 107-120 ◽  
Author(s):  
Meterfi Baroudi ◽  
Wael El Zerey ◽  
Salaheddine Bachir Bouiadjra
Keyword(s):  
Water Stress ◽  
Durum Wheat ◽  
Climatic Factors ◽  
Climatic Variability ◽  
Water Environment ◽  
Thermal Fluctuations ◽  
Reproductive Period ◽  
Large Variability ◽  
Semi Arid Region ◽  
North Western

In semi arid region of the South West of the Mediterranean basin, low rainfall, and thermal fluctuations cause water stress situations affecting at different levels, with varying intensities, the development of durum wheat yields. This work aims to study the major climatic factors that determine water environment of durum wheat in its reproductive period and assess their trend related to yields of the grain. Comparing diagrams of Bagnoul and Gaussen, established for two periods (1913-1937 and 1977-2014), highlighted an increase in the duration of the dry season due to rising temperatures, especially summer and a decrease in volume of the seasonal rainfall involving therefore water stress during the reproductive phase of cereal. The analysis of water regime in the past three decades, for the months of March, April and May, through the application of the approach of UNESCO-FAO, highlighted a very large variability in intensity of water stress during grain development period during the last years and also the tendency of the spring season months to be more drought. This reflects the complexity of the selection for yield components in this region. International Journal of Environment Vol. 5 (1) 2016,  pp: 107-120

scholarly journals Nitrile-Substituted 2-(Oxazolinyl)-Phenols: Minimalistic Excited-State Intramolecular Proton Transfer (ESIPT)-Based Fluorophores

2020 ◽  
Author(s):  
Dominik Göbel ◽  
Daniel Duvinage ◽  
Tim Stauch ◽  
Boris Nachtsheim
Keyword(s):  
Excited State ◽  
Solid State ◽  
Proton Transfer ◽  
Density Functional ◽  
Intramolecular Proton Transfer ◽  
Crystal Structure Analysis ◽  
Quantum Yields ◽  
Functional Theory ◽  
Emission Properties ◽  
Emission Enhancement

Herein, we present minimalistic single-benzene, excited-state intramolecular proton transfer (ESIPT) based fluorophores as powerful solid state emitters. The very simple synthesis gave access to all four regioisomers of nitrile-substituted 2(oxazolinyl)phenols (MW = 216.1). In respect of their emission properties they can be divided into aggregation-induced emission enhancement (AIEE) luminophores (1-CN and 2-CN), dual state emission (DSE) emitters (3-CN) and aggregation-caused quenching (ACQ) fluorophores (4‐CN). Remarkably, with compound 1-CN we discovered a minimalistic ESIPT based fluorophore with extremely high quantum yield in the solid state ΦF = 87.3% at λem = 491 nm. Furthermore, quantum yields in solution were determined up to ΦF = 63.0%, combined with Stokes shifts up till 11.300 cm–1. Temperature dependent emission mapping, crystal structure analysis and time-dependent density functional theory (TDDFT) calculations gave deep insight into the origin of the emission properties.<br>

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