scholarly journals Microsolvation of Histidine—A Theoretical Study of Intermolecular Interactions Based on AIM and SAPT Approaches

Symmetry ◽  
2020 ◽  
Vol 12 (7) ◽  
pp. 1153
Author(s):  
Beata Kizior ◽  
Jarosław J. Panek ◽  
Aneta Jezierska
Keyword(s):  
Gas Phase ◽  
Density Functional ◽  
Heterocyclic Ring ◽  
Polarizable Continuum Model ◽  
Water Molecules ◽  
Implicit Solvent ◽  
Actual Interaction ◽  
The Stability ◽  
Explicit Water ◽  
The Impact

Histidine is unique among amino acids because of its rich tautomeric properties. It participates in essential enzymatic centers, such as catalytic triads. The main aim of the study is the modeling of the change of molecular properties between the gas phase and solution using microsolvation models. We investigate histidine in its three protonation states, microsolvated with 1:6 water molecules. These clusters are studied computationally, in the gas phase and with water as a solvent (Polarizable Continuum Model, PCM) within the Density Functional Theory (DFT) framework. The structural analysis reveals the presence of intra- and intermolecular hydrogen bonds. The Atoms-in-Molecules (AIM) theory is employed to determine the impact of solvation on the charge flow within the histidine, with emphasis on the similarity of the two imidazole nitrogen atoms—topologically not equivalent, they are revealed as electronically similar due to the heterocyclic ring aromaticity. Finally, the Symmetry-Adapted Perturbation Theory (SAPT) is used to examine the stability of the microsolvation clusters. While electrostatic and exchange terms dominate in magnitude over polarization and dispersion, the sum of electrostatic and exchange term is close to zero. This makes polarization the factor governing the actual interaction energy. The most important finding of this study is that even with microsolvation, the polarization induced by the presence of implicit solvent is still significant. Therefore, we recommend combined approaches, mixing explicit water molecules with implicit models.

DFT STUDY OF THE PROTONATION AND DEPROTONATION ENTHALPIES OF BENZOXAZOLE, 1,2-BENZISOXAZOLE AND 2,1-BENZISOXAZOLE AND IMPLICATIONS FOR THE STRUCTURES AND ENERGIES OF THEIR ADDUCTS WITH EXPLICIT WATER MOLECULES

2013 ◽  
Vol 12 (07) ◽  
pp. 1350070 ◽  
Author(s):  
MWADHAM M. KABANDA ◽  
ENO E. EBENSO
Keyword(s):  
Hydrogen Bonds ◽  
Density Functional ◽  
Biologically Active ◽  
Basis Sets ◽  
Water Molecules ◽  
Intermolecular Hydrogen Bonds ◽  
Theoretical Approaches ◽  
Potential Applications ◽  
The Stability ◽  
Explicit Water

Benzoxazole, 1,2-benzisoxazole and 2,1-benzisoxazole are biologically active molecules with potential applications in drug design. Their interaction with aqueous medium in biological systems may be simulated by considering their interaction with explicit water molecules. Such studies provide information on the structures, energies and type of interactions stabilizing the resulting geometric systems. The objective of the current study was to utilize theoretical approaches to investigate the structures, stabilization energy and binding energy of benzoxazole–water, 1,2-benzisoxazole–water and 2,1-benzisoxazole–water complexes. The calculations were performed utilizing the density functional theory (DFT)/M06-2X/6-311 ++ G(d,p) method and the DFT/ωB97XD method with both the 6-311 ++ G(d,p) and the aug-cc-pVDZ basis sets. The results suggest that the stability of the different clusters depends on interrelated factors including the rings formed by intermolecular hydrogen bonds and the proton affinity (PA) or acidity of the atoms forming the intermolecular hydrogen bonds with the water molecules. A comparison across methods indicates that the results follow similar trends with different methods.

scholarly journals Predicting the UV–vis spectra of oxazine dyes

2011 ◽  
Vol 7 ◽  
pp. 432-441 ◽  
Author(s):  
Scott Fleming ◽  
Andrew Mills ◽  
Tell Tuttle
Keyword(s):  
Excitation Energy ◽  
Density Functional ◽  
Polarizable Continuum Model ◽  
Implicit Solvent ◽  
Continuum Approach ◽  
Excitation Energies ◽  
Functional Theory ◽  
Partial Charges ◽  
Td Dft ◽  
Polarizable Continuum

In the current work we have investigated the ability of time-dependent density functional theory (TD-DFT) to predict the absorption spectra of a series of oxazine dyes and the effect of solvent on the accuracy of these predictions. Based on the results of this study, it is clear that for the series of oxazine dyes an accurate prediction of the excitation energy requires the inclusion of solvent. Implicit solvent included via a polarizable continuum approach was found to be sufficient in reproducing the excitation energies accurately in the majority of cases. Moreover, we found that the SMD solvent model, which is dependent on the full electron density of the solute without partitioning into partial charges, gave more reliable results for our systems relative to the conductor-like polarizable continuum model (CPCM), as implemented in Gaussian 09. In all cases the inclusion of solvent reduces the error in the predicted excitation energy to <0.3 eV and in the majority of cases to <0.1 eV.

scholarly journals Computational Evidence Suggests That 1-chloroethanol May Be an Intermediate in the Thermal Decomposition of 2-chloroethanol into Acetaldehyde and HCl

2019 ◽  
Author(s):  
Zoi Salta ◽  
Agnie M. Kosmas ◽  
Oscar Ventura ◽  
Vincenzo Barone
Keyword(s):  
Aqueous Solution ◽  
Water Molecule ◽  
Gas Phase ◽  
Density Functional ◽  
Water Molecules ◽  
Functional Theory ◽  
Direct Transformation ◽  
The Density Functional Theory ◽  
Successive Step ◽  
The One

<p>The dehalogenation of 2-chloroethanol (2ClEtOH) in gas phase with and without participation of catalytic water molecules has been investigated using methods rooted into the density functional theory. The well-known HCl elimination leading to vinyl alcohol (VA) was compared to the alternative elimination route towards oxirane and shown to be kinetically and thermodynamically more favorable. However, the isomerization of VA to acetaldehyde in the gas phase, in the absence of water, was shown to be kinetically and thermodynamically less favorable than the recombination of VA and HCl to form the isomeric 1-chloroethanol (1ClEtOH) species. This species is more stable than 2ClEtOH by about 6 kcal mol<sup>-1</sup>, and the reaction barrier is 22 kcal mol<sup>-1</sup> vs 55 kcal mol<sup>-1</sup> for the direct transformation of VA to acetaldehyde. In a successive step, 1ClEtOH can decompose directly to acetaldehyde and HCl with a lower barrier (29 kcal mol<sup>-1</sup>) than that of VA to the same products (55 kcal mol<sup>-1</sup>). The calculations were repeated using a single ancillary water molecule (W) in the complexes 2ClEtOH_W and 1ClEtOH_W. The latter adduct is now more stable than 2ClEtOH_W by about 8 kcal mol<sup>-1</sup>, implying that the water molecule increased the already higher stability of 1ClEtOH in the gas phase. However, this catalytic water molecule lowers dramatically the barrier for the interconversion of VA to acetaldehyde (from 55 to 6 kcal mol<sup>-1</sup>). This barrier is now smaller than the one for the conversion to 1ClEtOH (which also decreases, but not so much, from 22 to 12 kcal mol<sup>-1</sup>). Thus, it is concluded that while 1ClEtOH may be a plausible intermediate in the gas phase dehalogenation of 2ClEtOH, it is unlikely that it plays a major role in water complexes (or, by inference, aqueous solution). It is also shown that neither in the gas phase nor in the cluster with one water molecule, the oxirane path is competitive with the VA alcohol path.</p>

scholarly journals Н-комплексы 1,2-нафтохинона с молекулами воды в водном растворе и их влияние на сдвиги полос поглощения

2021 ◽  
Vol 129 (5) ◽  
pp. 599
Author(s):  
С.Н. Цеплина ◽  
E.E. Цеплин
Keyword(s):  
Quantum Chemical ◽  
Continuum Model ◽  
Density Functional ◽  
Water Solution ◽  
Polarizable Continuum Model ◽  
Water Molecules ◽  
Absorption Bands ◽  
Functional Theory ◽  
Polarizable Continuum ◽  
Polar Water

Optical absorption spectra of 1,2-naphthoquinone in non-polar (n-hexane) and polar (water) solvents were obtained. It is shown that the use of quantum chemical calculations based on time-dependent density functional theory (TDDFT B3LYP/6-311+G(d, p)) with the polarizable continuum model (PCM) for calculating 1,2-naphthoquinone in a solution of n-hexane and hydrogen complex of 1,2-naphthoquinone with two water molecules in an aqueous medium describes well the shifts of the absorption bands of 1,2-naphthoquinone in a water solution compared to a solution in n-hexane. Based on the analysis of deviations of the calculated band shifts from the experimental ones, the question of the formation of 1,2-naphthoquinone hydrogen complexes with n water molecules (n = 1-4) in an aqueous solution is considered.

The impact of cation–π, anion–π, and CH–π interactions on the excited-state intramolecular proton transfer of 1,4-dihydroxyanthraquinone

2021 ◽  
Author(s):  
Asiyeh Shahraki ◽  
Ali Ebrahimi ◽  
Shiva Rezazadeh ◽  
Roya Behazin
Keyword(s):  
Density Functional Theory ◽  
Gas Phase ◽  
Density Functional ◽  
Photophysical Properties ◽  
Intramolecular Proton Transfer ◽  
Time Dependent ◽  
Functional Theory ◽  
The Density Functional Theory ◽  
The Impact ◽  
Dependent Density

The impact of ion-π interactions on the photophysical properties of quinizarin have been investigated using the density functional theory and time-dependent density functional theory at the M06-2X/6-311++G(d,p) level in the gas phase and solution.

Exploring halide anion affinities to native cyclodextrins by mass spectrometry and molecular modelling

2017 ◽  
Vol 24 (3) ◽  
pp. 269-278 ◽  
Author(s):  
Chongsheng Xu ◽  
Nan He ◽  
Zhenhua Li ◽  
Yanqiu Chu ◽  
Chuan-Fan Ding
Keyword(s):  
Gas Phase ◽  
Density Functional ◽  
Binding Constants ◽  
Density Functional Theory Calculations ◽  
Collision Induced Dissociation ◽  
Binding Affinities ◽  
Cyclodextrin Complex ◽  
Halide Anion ◽  
Mass Frame ◽  
The Stability

The binding affinities of cyclodextrins complexation with chlorine (Cl−), bromine (Br−) and iodine (I−), were measured by mass spectrometric titrimetry, and the fitting of the binding constants was based on the concentration measurement of the cyclodextrin equilibrium. The binding constants (lg Ka) for α-, β- or γ-cyclodextrin with Cl− were 3.99, 4.03 and 4.11, respectively. The gas-phase binding affinity of halide anions for native cyclodextrins was probed by collision-induced dissociation. In collision-induced dissociation, the centre-of-mass frame energy results revealed that in the gas phase, for the same type of cyclodextrin, the stability of the complexes decreased in order: Cl > Br > I, and for the same halide anion, the binding stability of the complex with α-, β- or γ-cyclodextrin decreased in the order: γ-cyclodextrin >β-cyclodextrin > α-cyclodextrin. The density functional theory calculations showed that halide anion binding on the primary face had a lower energy than the secondary face and hydrogen bonding was the main driving force for complex formation. The higher stability of the γ-cyclodextrin complex with the Cl anion can be attributed to the higher charge density of the Cl anion and better flexibility of γ-cyclodextrin.

A SELF-CONSISTENT-CHARGE DENSITY-FUNCTIONAL TIGHT-BINDING THEORY BASED MOLECULAR DYNAMICS SIMULATION OF A ZWITTERIONIC GLYCINE IN AN EXPLICIT WATER ENVIRONMENT

2013 ◽  
Vol 12 (04) ◽  
pp. 1350019 ◽  
Author(s):  
Y. ZHAI ◽  
Y. L. ZHAO
Keyword(s):  
Molecular Dynamics ◽  
Amino Acids ◽  
Charge Density ◽  
Density Functional ◽  
Water Environment ◽  
Tight Binding ◽  
Water Molecules ◽  
Binding Theory ◽  
Self Consistent ◽  
The Impact

A zwitterionic glycine (zGLY) is adopted as an example to study the impact of water environment (310 H2O molecules) on the molecular structure and energetics using a self-consistent-charge density-functional tight-binding theory based molecular dynamics (SCC-DFTB/MD) method. It is found that maximal eight hydrogen bonds could be formed simultaneously between eight water molecules and the zGLY. The ability of the COO- terminal to adsorb water molecules is stronger than the [Formula: see text] terminal with respect to hydrogen bonding with more water molecules and exhibits lower adiabatic adsorption energies. The zGLY's intramolecular hydrogen bond appeared unpredictably, without involving any proton transfer and generally helpful for enhancing the system stability. Water molecules play an important role to stabilize the zwitterionic amino acids and restrain the proton migration from the [Formula: see text] to the COO− group. Our results show that the SCC-DFTB/MD method could successfully describe geometry dynamical evolutions and energetics of biomolecules in a nanoscale simulation with the presence of a large number of water molecules. Our study not only verified the feasibility of a QM level methodology for describing the aqueous states of biochemical molecules, but also gave a clear evidence for the impact of water environment on amino acids.

A density functional theory study of the hydration of calcium ions confined in the interlayer space of montmorillonites

2014 ◽  
Vol 13 (04) ◽  
pp. 1450028 ◽  
Author(s):  
Zhaoyang Lou ◽  
Houbin Liu ◽  
Yao Zhang ◽  
Yingfeng Meng ◽  
Qun Zeng ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Gas Phase ◽  
Density Functional ◽  
Interlayer Space ◽  
Negative Charge ◽  
Internal Surface ◽  
Water Molecules ◽  
Surrounding Water ◽  
Functional Theory ◽  
Internal Surfaces

The structures of Ca2+hydrates in the interlayer space of montmorillonites (MMT) were studied by periodic density functional theory (DFT) calculations under the GGA/PBE approximation. Affected by the internal surfaces, which are rich of negative charge, the Ca2+hydration exhibits different behaviors from that in gas phase. The Ca2+is located at the six-oxygen-ring (SOR) on the internal surface in dry MMT, while the incoming water molecules bind with the Ca2+, the O atoms on surface, and/or with each other. The water molecules have a tendency of forming a hydrogen bond (HB) network that connects the upper and lower surfaces. Attracted by surrounding water molecules, the Ca2+gradually moves outward with increasing number of water molecules. Moreover, the hydration energy (EH) of Ca2+is determined not only by the interaction between Ca2+and H2O , but also by that among Ca2+, H2O and the surfaces. As a result, the EHhas only small changes for additional incoming water molecules, in contrast to the great and monotonic decrease in gas phase.

Comparative theoretical studies of dinitromethyl- or trinitromethyl-modified derivatives of CL-20

2013 ◽  
Vol 91 (12) ◽  
pp. 1243-1251 ◽  
Author(s):  
Yong Pan ◽  
Weihua Zhu ◽  
Heming Xiao
Keyword(s):  
Thermal Stability ◽  
Density Functional ◽  
Parent Compound ◽  
Initial Step ◽  
Impact Sensitivity ◽  
Detonation Properties ◽  
Energetic Properties ◽  
The Stability ◽  
The Impact ◽  
Trinitromethyl Group

The heats of formation (HOFs), energetic properties, strain energies, thermal stability, and impact sensitivity for a series of trinitromethyl- or dinitromethyl-modified CL-20 derivatives were studied by using density functional theory. It is found that the trinitromethyl group is an effective structural unit for improving the gas-phase HOFs and energetic properties of the derivatives. However, incorporating the dinitromethyl group into the parent compound is not favorable for increasing its HOFs and detonation properties. The effects of the dinitromethyl or trinitromethyl groups on the stability of the parent compound are discussed. The studies on strain energies show that the introduction of the trinitromethyl group intensifies the strain of the cage skeleton for the title compounds, whereas for the dinitromethyl groups, the case is quite the contrary. An analysis of the bond dissociation energies for several relatively weak bonds suggests that the substitution of the dinitromethyl or trinitromethyl group decreases the thermal stability of the derivatives. The C−NO2 bond in the dinitromethyl or trinitromethyl group is the weakest one and the homolysis of the C−NO2 bond may be the initial step in thermal decomposition. In addition, according to the calculated free space per molecule, the introduction of the dinitromethyl or trinitromethyl group increases the impact sensitivities of the derivatives. Considering the detonation performance, thermal stability, and impact sensitivity, six compounds can be regarded as the target high-energetic compounds.

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