Origin of the Absorption Band of Bromophenol Blue in Acidic and Basic pH: Insight from a Combined Molecular Dynamics and TD-DFT/MM Study

We study the linear and nonlinear optical properties of a well-known acid–base indicator, bromophenol blue (BPB), in aqueous solution by employing static and integrated approaches. In the static approach, optical properties have been calculated using time-dependent density functional theory (TD-DFT) on the fully relaxed geometries of the neutral and different unprotonated forms of BPB. Moreover, both closed and open forms of BPB were considered. In the integrated approach, the optical properties have been computed over many snapshots extracted from molecular dynamics simulation using a hybrid time-dependent density functional theory/molecular mechanics approach. The static approach suggests closed neutral ⇒ anionic interconversion as the dominant mechanism for the red shift in the absorption spectra of BPB due to a change from acidic to basic pH. It is found by employing an integrated approach that the two interconversions, namely open neutral ⇒ anionic and open neutral ⇒ dianionic, can contribute to the pH-dependent shift in the absorption spectra of BPB. Even though both static and integrated approaches reproduce the pH-dependent red shift in the absorption spectra of BPB, the latter one is suitable to determine both the spectra and spectral broadening. Finally, the computed static first hyperpolarizability for various protonated and deprotonated forms of BPB reveals that this molecule can be used as a nonlinear optical probe for pH sensing in addition to its highly exploited use as an optical probe

Solvent Polarity-Induced Conformational Unlocking of Asparagine

Classical and Car–Parrinello molecular dynamics simulations are performed to study the solvent effect on the conformational distribution of asparagine. Conformational populations obtained from the simulations in gas phase and in nonpolar chloroform solvent are in agreement with the most probable single conformation of asparagine in the gas phase measured in recent laser ablation with molecular beam Fourier transform microwave spectroscopy experiments. We rationalize that intramolecular hydrogen bonding and dipole–dipole interactions between carbonyl groups dictate such a conformational locking to a single asparagine conformer. The solvent polarity induced interlocking or intermolecular hydrogen bonding with water solvent molecules destabilizes the (NH···OC) bonding between side chain and terminal groups of asparagine, while not essentially affecting the (NH···OC) intramolecular hydrogen bondings within the side chain nor within the terminal groups. Such a conformational unlocking or cage effect is observed in asparagine within aqueous solution. We observed a spontaneous conversion of neutral to zwitterionic isomer of asparagine in aqueous solution, which is in agreement with interpretation of Raman spectroscopy results. Using Møller–Plesset second order perturbation theory, we show that a tautomeric shift from neutral to zwitterionic occurs on asparagine in between DMSO and water solvents. The ramification of these findings for the conformational character of asparagine is briefly discussed

Studies of pH-Sensitive Optical Properties of the deGFP1 Green Fluorescent Protein Using a Unique Polarizable Force Field

The aim of this study is to identify the responsible molecular forms for the pH dependent optical properties of the deGFP1 green fluorescent protein mutant. We have carried out static and dynamic type calculations for all four protonation states of the chromophore to unravel the contributions due to finite temperature and the flexible protein backbone on the pH dependent optical properties. In particular, we have used a combined molecular dynamics and density functional–molecular mechanics linear response approach by means of which the optical property calculations were carried out for the chromophore in the explicitly treated solvent and bioenvironment. Two different models were used to describe the environmentelectronic embedding and polarizable electronic embeddingaccounting for the polarization of the chromophore and the mutual polarization between the chromophore and the environment, respectively. For this purpose a polarizable force field was derived quantum mechanically for the protein environment by use of analytical response theory. While the gas-phase calculations for the chromophore predict that the induced red shift going from low to high pH is attributed to the change of molecular forms from neutral to zwitterionic, the two more advanced models that explicitly account for the protein backbone attribute the pH shift to a neutral to anionic conversion. Some ramifications of the results for the use of GFPs as pH sensors are discussed

Chelation-Induced Quenching of Two-Photon Absorption of Azacrown Ether Substituted Distyryl Benzene for Metal Ion Sensing

Imaging of metal ion concentration, distribution, and dynamics can pave the way to diagnose a number of diseases and to identify the normal functioning of the human body. Recently, two-photon microscopy-based imaging of metal ions has become popular due to several favorable factors as compared to fluorescence-based imaging. However, much has to be investigated in order to design probes with large two-photon absorption cross sections and yet with selective binding affinity toward metal ions. In particular, it is crucial to recognize the mechanisms of metal ion-induced changes of the two-photon absorption intensity. The present paper contributes to this effort and reports on the results of extensive studies carried out to define a reliable computational protocol that can account for sampling, solvent, and finite temperature effects for one- and two-photon properties of metal probes, using azacrown ether substituted distyrylbenzene embedded in solvents as a testbed. We employ a selection of theoretical approaches to model the structure of the probe alone and in the presence of Mg²⁺ ion in acetonitrile solvent, including static quantum-chemical calculations, rigid- and flexible-body molecular dynamics, and hybrid QM/MM molecular dynamics. For a set of solute–solvent configurations, the one- and the two-photon properties are computed using the recently developed polarizable embedding response approach. It is found that the hybrid QM/MM molecular dynamics based approach is the most successful one among other employed computational strategies, viz. reproduction of the metal ion-induced blue shift in the absorption wavelength and decrease in the two-photon absorption cross section, which actually is in excellent agreement with experimental data. The mechanism for such metal ion-induced changes in the optical properties is put forward using a few-state model. Possible design principles to tune the two-photon absorption properties of probes are also discussed

Investigation into Biological Environments through (Non)linear Optics: A Multiscale Study of Laurdan Derivatives

The fluorescent marker Laurdan and its new derivative, C-Laurdan, have been investigated by means of theoretical calculations in a DOPC lipid bilayer membrane at room temperature, and a comparison is made with results from fluorescence experiments. Experimentally, the latter probe is known to have a higher sensitivity to the membrane polarity at the lipid headgroup region and has higher water solubility. Results from Molecular Dynamics (MD) simulations show that C-Laurdan is oriented with the carboxyl group toward the head of the membrane, with an angle of 50° between the molecular backbone and the normal to the bilayer, in contrast to the orientation of the Laurdan headgroup whose carbonyl group is oriented toward the polar regions of the membrane and which describes an angle of ca. 70–80° with the membrane normal. This contrast in orientation reflects the differences in transition dipole moment between the two probes and, in turn, the optical properties. QM/MM results of the probes show little differences for one- (OPA) and two-photon absorption (TPA) spectra, while the second harmonic generation (SHG) beta component is twice as large in Laurdan with respect to C-Laurdan probe. The fluorescence anisotropy decay analysis of the first excited state confirms that Laurdan has more rotational freedom in the DOPC membrane, while C-Laurdan experiences a higher hindrance, making it a better probe for lipid membrane phase recognition

The Culprit Is in the Cave: The Core Sites Explain the Binding Profiles of Amyloid-Specific Tracers

The design of molecular probes and tracer molecules with specificity toward amyloid beta (Aβ) fibrils is of paramount importance for the selective diagnosis of Alzheimer’s disease. This requires a detailed understanding of the binding sites in amyloid targets, their number, and their binding mechanism for various tracer molecules. We adopt an integrated approach including molecular docking, molecular dynamics, and generalized Born-based free energy calculations to investigate site-specific interactions of different amyloid binding molecules. Our study reproduces the experimental results on the relative binding affinity of the tracers and amyloid binders and explains the feature of “multiple binding sites” in amyloid targets as probed by competition binding experiments. A major outcome of this study is that it is the core sites of the Aβ fibrils that are responsible for the experimentally reported binding profiles of tracers in amyloid targets rather than the surface sites that received much focus in earlier investigations

Association Dynamics and Linear and Nonlinear Optical Properties of an <i>N</i>‑Acetylaladanamide Probe in a POPC Membrane

Along with the growing evidence that relates membrane abnormalities to various diseases, biological membranes have been acknowledged as targets for therapy. Any such abnormality in the membrane structure alters the membrane potential which in principle can be captured by measuring properties of specific optical probes. There exists by now many molecular probes with absorption and fluorescence properties that are sensitive to local membrane structure and to the membrane potential. To suggest new high-performance optical probes for membrane-potential imaging it is important to understand in detail the membrane-induced structural changes in the probe, the membrane association dynamics of the probe, and its membrane-specific optical properties. To contribute to this effort, we here study an optical probe, <i>N</i>-acetylaladanamide (NAAA), in the presence of a POPC lipid bilayer using a multiscale integrated approach to assess the probe structure, dynamics, and optical properties in its membrane-bound status and in water solvent. We find that the probe eventually assimilates into the membrane with a specific orientation where the hydrophobic part of the probe is buried inside the lipid bilayer, while the hydrophilic part is exposed to the water solvent. The computed absorption maximum is red-shifted when compared to the gas phase. The computations of the two-photon absorption and second harmonic generation cross sections of the NAAA probe in its membrane-bound state which is of its first kind in the literature suggest that this probe can be used for imaging the membrane potential using nonlinear optical microscopy

Amyloid Fibril-Induced Structural and Spectral Modifications in the Thioflavin‑T Optical Probe

Motivated by future possibilities to design target molecules for fibrils with diagnostic or therapeutic capability related to amyloidosis diseases, we investigate in this work the dielectric nature of amyloid fibril microenvironments in different binding sites using an optical probe, thioflavin-T (THT), which has been used extensively to stain such fibrils. We study the fibril-environment-induced structural and spectral changes of THT at each binding site and compare the results to the fibril-free situation in aqueous solution. All binding sites are found to show a similar effect with respect to the conformational changes of THT; in the presence of the fibril, its molecular geometry tends to become planarized. However, depending on the dielectric nature of the specific binding site, a red shift, blue shift, or no shift in the absorption spectra of THT is predicted. Interestingly, the experimentally measured red shift in the spectra is seen only when THT binds to one of the core or surface-binding sites. It is found that the dielectric nature of the microenvironment in the fibril is strongly nonhomogeneous

Amyloid Fibril-Induced Structural and Spectral Modifications in the Thioflavin‑T Optical Probe

Motivated by future possibilities to design target molecules for fibrils with diagnostic or therapeutic capability related to amyloidosis diseases, we investigate in this work the dielectric nature of amyloid fibril microenvironments in different binding sites using an optical probe, thioflavin-T (THT), which has been used extensively to stain such fibrils. We study the fibril-environment-induced structural and spectral changes of THT at each binding site and compare the results to the fibril-free situation in aqueous solution. All binding sites are found to show a similar effect with respect to the conformational changes of THT; in the presence of the fibril, its molecular geometry tends to become planarized. However, depending on the dielectric nature of the specific binding site, a red shift, blue shift, or no shift in the absorption spectra of THT is predicted. Interestingly, the experimentally measured red shift in the spectra is seen only when THT binds to one of the core or surface-binding sites. It is found that the dielectric nature of the microenvironment in the fibril is strongly nonhomogeneous

<i>In silico</i> modeling and experimental evidence of coagulant protein interaction with precursors for nanoparticle functionalization

<div><p>The design of novel protein–nanoparticle hybrid systems has applications in many fields of science ranging from biomedicine, catalysis, water treatment, etc. The main barrier in devising such tool is lack of adequate information or poor understanding of protein–ligand chemistry. Here, we establish a new strategy based on computational modeling for protein and precursor linkers that can decorate the nanoparticles. <i>Moringa oleifera</i> (MO_2.1) seed protein that has coagulation and antimicrobial properties was used. Superparamagnetic nanoparticles (SPION) with precursor ligands were used for the protein–ligand interaction studies. The molecular docking studies reveal that there are two binding sites, one is located at the core binding site; tetraethoxysilane (TEOS) or 3-aminopropyl trimethoxysilane (APTES) binds to this site while the other one is located at the side chain residues where trisodium citrate (TSC) or Si₆₀ binds to this site. The protein–ligand distance profile analysis explains the differences in functional activity of the decorated SPION. Experimentally, TSC-coated nanoparticles showed higher coagulation activity as compared to TEOS- and APTES-coated SPION. To our knowledge, this is the first report on <i>in vitro</i> experimental data, which endorses the computational modeling studies as a powerful tool to design novel precursors for functionalization of nanomaterials; and develop interface hybrid systems for various applications.</p> </div