Stability and IR Spectroscopy of Zwitterionic Form of β-Alanine in Water Clusters

Ghassemizadeh, Reyhaneh; Moore, Brendan; Momose, Takamasa; Walter, Michael

doi:10.1021/acs.jpcb.9b00654

Cited by 12 publications

(16 citation statements)

References 51 publications

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“…Nevertheless, the "trapped water" molecule is in similar spirit as the "connecting water" molecule in the recent experimental and theoretical findings. 37 Crittenden et al 15 also found a molecular bridge of one or two water molecules for GABA• 2H 2 O and GABA•5H 2 O. Thus, the results of the current study capture some of the features of existing studies.…”

Section: Resultssupporting

confidence: 80%

“…We note here that, although the favorable electrostatics have the tendency to trap more water molecules, spatial constraints forbid the same. A recent experimental and theoretical study 37 on microsolvated β-alanine shows the existence of "connecting water" between the carboxylate and amino groups. The "connecting water", which is similar to the trapped water molecule in the current study, is found to enhance the stability of the zwitterionic β-alanine.…”

Section: Resultsmentioning

confidence: 99%

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Conformation-Induced Dynamical Heterogeneity of Water in the Solvation Shell of Zwitterionic γ-Aminobutyric Acid

Sharma

Chandra

2019

J. Phys. Chem. B

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The structure and dynamics of water molecules around the carboxylate and amino groups of γ-aminobutyric acid (GABA), a primary neurotransmitter in mammals, are investigated by means of ab initio molecular dynamics simulation. Zwitterionic GABA has two major conformations in water, namely, the open and the closed conformations. The angle-averaged one-dimensional structures of water in the solvation shells around the carboxylate and amino groups are found to be quite similar for the closed and open conformations of the solute. The two-dimensional structural correlations, which describe the solvation shell structure with better resolution, reveal some differences in the arrangement of water molecules around the solute for its open and closed conformations. It is found that the dynamics of solvation shells in the two conformations vary only slightly. However, the existence of trapped water between the oppositely charged carboxylate and amino groups of GABA in its closed form is found to give rise to a very different dynamical behavior as compared to the overall solvation shell in the same conformation as well as that in the open conformation. Thus, dynamical heterogeneity at a local level is induced by a change in the conformation of zwitterionic GABA. Such trapped water is not seen in the open form of the solute. A similar type of “connecting water” has also been observed for microsolvated β-alanine in a recent experimental and theoretical study ( Ghassemizadeh Ghassemizadeh J. Phys. Chem. B201912343924399). Thus, the current study shows the variation of binding properties of water with the change in the conformation of zwitterionic GABA, which in turn changes the dynamics of water at a local level. The conformation-induced changes in the water dynamics constitute an example of dynamical heterogeneity of water, which is normally observed in the presence of large biomolecules like proteins, DNA, etc.

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Section: Resultssupporting

confidence: 80%

Section: Resultsmentioning

confidence: 99%

Conformation-Induced Dynamical Heterogeneity of Water in the Solvation Shell of Zwitterionic γ-Aminobutyric Acid

Sharma

Chandra

2019

J. Phys. Chem. B

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“…The huge amount of water at the earth's surface supports a multitude of dissolved gases and nano-particles that are significant in climate change; cf., for instance, black carbon [2]. Further issues related to water are the behaviour of oil films [3], the synthesis of nano-materials for medical applications [4,5], the behaviour of two-dimensional materials [6], and the behaviour of colloidal suspensions [7,8]. The functional mechanism of membranes [9,10] is also a relevant class.…”

Section: Introductionmentioning

confidence: 99%

“…The huge amount of water at the earth’s surface supports a multitude of dissolved gases and nanoparticles that are significant in climate change, cf., for instance, black carbon . Further issues related to water are the spreading of oil films, synthesis of nanomaterials for medical applications, , formation of two-dimensional materials, and stability of colloidal suspensions. , The functional mechanism of membranes , is also a relevant class. The description of all these systems requires good knowledge of the dielectric function of water on the real frequency axis as well as, for calculation of van der Waals interactions, imaginary frequencies.…”

Section: Introductionmentioning

confidence: 99%

Full-Spectrum High-Resolution Modeling of the Dielectric Function of Water

et al. 2020

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In view of the vital role of water in chemical and physical processes, an exact knowledge of its dielectric function over a large frequency range is important. In this article we report on currently available measurements of the dielectric function of water at room temperature (25 • C) across the full electromagnetic spectrum: microwave, IR, UV and X-ray (up to 100 eV). We provide parameterisations of the complex dielectric function of water with two Debye (microwave) oscillators and high resolution of IR and UV/X-ray oscillators. We also report dielectric parameters for ice-cold water with a microwave/IR spectrum measured at 0.4 • C, while taking the UV spectrum from 25 • C (assuming negligible temperature dependence in UV). We illustrate the consequences of the model via calculations of van der Waals interactions of gas molecules near water surfaces, and an assessment of the thickness of water films on ice and ice films on water. In contrast to earlier models of ice-cold water, we predict that a micron-scale layer of ice is stabilised on a bulk water surface. Similarly, the van der Waals interaction promotes complete freezing rather than supporting a thin premelting layer of water on a bulk ice surface. Density-based extrapolation from warm to cold water of the dielectric function at imaginary frequencies is found to be satisfactory in the microwave but poor (40% error) at IR frequencies.

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“…In this report, a discrete model was selected by using IR spectroscopy and DFT calculations of tryptophan structures in their zwitterionic form within clusters of Trp-(H 2 O) n with n ≥ 5 [12]. For β-Alanine, Ghassemizadeh et al [16] show a direct transfer of protons from the amino group to the carboxyl group with five and six molecules of water, which change the Trp molecule from a neutral to a zwitterionic form, thereby leading to two bonds that give rise to the COO − and 3 NH + components. These molecules of water form as many hydrogen bonds as possible between them and the zwitterion, so that an additional hydrogen-bonded wire is formed between the charged poles with seven and eight molecules of water.…”

Section: Introductionmentioning

confidence: 99%

Redshift of Excitation Wavelength Caused by the Concentration of L-Tryptophan in Water: A Theoretical and Experimental Study

Uriza-Prias¹,

Méndez-Blas²,

Rivas-Silva³

2021

OJPC

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A redshift in the wavelength of excitation spectra is experimentally measured as a function of the concentration parameter for tryptophan solutions in water. To understand the microscopic causes of this behavior, theoretical calculations obtained from four model clusters are carried out: 36 , where there are interactions among 1, 2, 3 and 4 molecules of tryptophan. According to the literature, each interaction occurred with nine molecules of water to stabilize its expected zwitterionic form. In these models, the molecules of tryptophan appear at an adjacent distance among them to generate an analogous behavior when there is an experimental increase in the concentration. It is evident that the distance between adjacent molecules of tryptophan decreases as their concentration increases. The optical properties of these clusters are obtained by studying the corresponding excited states and the molecular orbitals involved, showing charge transfers by using time-dependent density functional theory (TD-DFT) methods. The experimental spectroscopic data are obtained by using the clusters proposed, and good agreement is found by drawing a comparison with the theoretical data.

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Stability and IR Spectroscopy of Zwitterionic Form of β-Alanine in Water Clusters

Cited by 12 publications

References 51 publications

Conformation-Induced Dynamical Heterogeneity of Water in the Solvation Shell of Zwitterionic γ-Aminobutyric Acid

Conformation-Induced Dynamical Heterogeneity of Water in the Solvation Shell of Zwitterionic γ-Aminobutyric Acid

Full-Spectrum High-Resolution Modeling of the Dielectric Function of Water

Redshift of Excitation Wavelength Caused by the Concentration of L-Tryptophan in Water: A Theoretical and Experimental Study

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