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Special Issue "Small Molecule Near Infrared Contrast Agents: Synthesis and Applications"

A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Organic Chemistry".

Deadline for manuscript submissions: 30 September 2018

Special Issue Editor

Guest Editor
Prof. Maged Henary

Chemistry department, Georgia State University, Atlanta, GA 30303, USA
Website | E-Mail
Interests: organic synthesis; heterocyclic chemistry; fluorescent probes; NIR contrast agents; metal sensors; microwave synthesis; biomedical applications; bioanalytical applications

Special Issue Information

Dear Colleagues,

Near-Infrared (NIR) absorbing fluorophores have become important as diagnostic and therapeutic agents in the field of tumor research, with the number of related publications having skyrocketed throughout the last few years. The utilization of the NIR spectral region (650–900 nm) is advantageous due to the inherently lower background interference, which makes it well suited for techniques analyzing high complexity samples and for many applications.

This Special Issue is focusing on “Small Molecule NIR Contrast Agents” within topic-related chapters, dealing with all aspects, such as synthesis, structure, complexity, optical properties, reactivity, stability and applications in material science, imaging, biomedical, and bioanalytical applications. Review articles by experts in the field will also be welcome.

Prof. Maged Henary
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All papers will be peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Molecules is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1800 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.


  • synthesis of NIR contrast agents
  • optical properties, reactivity, and stability of NIR fluorophores
  • NIR fluorophores interaction with Biomolecules
  • NIR Fluorescent sensors (metals, enzymatic, etc.)
  • biomedical applications
  • bioanalytical applications
  • biomolecular imaging (NIR for image-guided surgery)

Published Papers (1 paper)

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Open AccessFeature PaperArticle Fluorescent Thienothiophene-Containing Squaraine Dyes and Threaded Supramolecular Complexes with Tunable Wavelengths between 600–800 nm
Molecules 2018, 23(9), 2229; https://doi.org/10.3390/molecules23092229
Received: 15 August 2018 / Revised: 28 August 2018 / Accepted: 31 August 2018 / Published: 1 September 2018
PDF Full-text (7980 KB) | HTML Full-text | XML Full-text | Supplementary Files
A new family of fluorescent thiophene and thienothiophene-containing squaraine dyes is described with tunable wavelengths that cover the absorption/emission range of 600–800 nm. The deep-red and near-infrared fluorescent compounds were easily prepared by simple synthesis and purification methods. Spectral studies showed that each
[...] Read more.
A new family of fluorescent thiophene and thienothiophene-containing squaraine dyes is described with tunable wavelengths that cover the absorption/emission range of 600–800 nm. The deep-red and near-infrared fluorescent compounds were easily prepared by simple synthesis and purification methods. Spectral studies showed that each squaraine was rapidly encapsulated by a tetralactam macrocycle, with nanomolar affinity in water, to produce a threaded supramolecular complex with high chemical stability, increased fluorescence quantum yield, and decreased fluorescence quenching upon dye self-aggregation. Energy transfer within the supramolecular complex permitted multiplex emission. That is, two separate dyes with fluorescence emission bands that match the popular Cy5 and Cy7 channels, could be simultaneously excited with a beam of 375 nm light. A broad range of practical applications is envisioned in healthcare diagnostics, microscopy, molecular imaging, and fluorescence-guided surgery. Full article

Graphical abstract

Planned Papers

The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.

Title: Determination of total carotenoid and phenolic content in blackberries (/Rubus fructicosus/L. ) combining near infrared spectroscopy (NIRS) and multivariate analysis
Author: Mercedes del Río Celestino
Abstract: A quick method to determine the content of phenolic compounds (TPC) and total carotenoid content (TCC) in blackberries based on near infrared spectroscopy (NIRS) was studied aiming to provide reductions of cost and analysis time for the food industry. A total of 106 samples were analyzed by the Folin-Ciocalteu method for TPC analysis and the method based in UV-Vis Spectrometer for TCC analysis. The average contents of TPC and TCC found were 24.27 mg g^-1 dwand 8.30 µg g^-1 dwrespectively. Modified partial least squares (MPLS) regression was used for obtaining the calibration models of the compounds. The RPD values from external validation (ratio of the standard deviation of the reference data to the standard error of prediction) for both TPC and TCC was between 1.5<RPD_p <2.5 and RER values (ratio of the range in the reference data to SEP) was 5.92 for TPC and 8.63 for TCC. These values showed that both equations to predictive ability were suitable for screening purposes. MPLS loading plots corresponding to the first terms of the equations showed the influence of sugars, chlorophyll, lipids and cellulose in the modelling of prediction equations.

Title: Ultra-bright and Stable Near-infrared Fluorescent Squaraine  Dyes
Author: Maged Henary
: Highly stable symmetric and asymmetric squaraine fluorophores have been synthesized featuring an internal salt bridge between a quaternary ammonium cation and the central oxycyclobutenolate ring of the chromophore.  The newly synthesized symmetric and asymmetric compounds display increased molar absorptivity (DMSO: symmetric average 447,325 M-1cm-1 and asymmetric average 333,725 M-1cm-1; Fetal Bovine Serum: 398,050 M-1cm-1 and 375,100 M-1 cm-1, respectively), quantum yield in serum (symmetric average ε = 45%, asymmetric average  ε = 79%), and thermal/photochemical stability over previously reported squaraine based dyes.  Consequently, both classes show great promise in re-surfacing the normally environment-labile squaraine dyes as novel imaging agents and scaffolds for fluorescence sensing. Furthermore, incorporating a covalent attachment point away from the conjugated system allows for biological tagging applications without disturbing the optimum optical characteristics of the newly designed fluorophore.

Title: Fluorescent thiophene and thienothiophene-containing squaraine dyes with tunable wavelengths from 500 nm to 875 nm and supramolecular encapsulation capabilities
Author: Bradly Smith
Abstract: A new family of fluorescent thiophene and thienothiophene-containing squaraine dyes is described with tunable wavelengths that cover the absorption/emission range from 500 nm to 875 nm. These novel squaraine dyes are synthetically flexible with easy synthesis and purification. Moreover, the squaraines can be rapidly encapsulated by a tetralactam macrocycle with very strong affinity in water to produce a supramolecular complex with increased fluorescence quantum yield and decreased propensity for dye self-aggregation. Energy transfer within the supramolecular complex permits multiplex imaging using a single UV excitation band with two orthogonal fluorescence emission windows that match the popular Cy5 and Cy7 filter sets. A wide set of practical applications are envisioned in healthcare diagnostics, molecular imaging, and fluorescence guided surgery.

Title: A Near-infrared Fluorescent Probe Based on FRET from Near-infrared Rhodamine Donor to Near-infrared Cyanine Acceptor for Double-Checked Sensitive Detection of Intracellular pH Changes
Author: Haiying Liu
Abstract: A near-infrared fluorescent probe has been developed by conjugating near-infrared rhodamine donor to near-infrared cyanine acceptor for double-checked sensitive detection of intracellular pH changes based on a FRET strategy.  Under a basic condition, the probe shows only weak fluorescence of cyanine acceptor with the rhodamine donor keeping its non-fluorescent closed spirolactam ring structure.  Gradual pH decreases lead to both graduate fluorescence increases of the rhodamine donor and cyanine acceptor at 650 nm and 780 nm, which can provide accurately double-checked sensitive detection of pH changes.  The probe has been applied to sensitively detect intracellular pH changes and fluctuations under oxidative stress and drug stimulus.  

Title: NIR-dyes for site-specific labeling of proteins
Author: Kevin Burgess
Abstract: A method for conveniently labeling thiol residues in proteins with a near-IR dye is presented.  Selectivity of the dye-electrophile for thiol groups over amino groups was established by gel electrophoresis and kinetics experiments.

Title: Counter Ion Effect on NIR Emission from Indolizine-based Cyanine Dyes
Author: Jared Delcamp
Abstract: A series of 6 NIR absorbing indolizine-based cyanine dyes with varying counter ions based on size, dipole and hydrophilicity have been analyzed in solution and as solid state films. While the absorption of these materials remained consistent in wavelength and molar absorptivity, the emission quantum yields and wavelengths were found to vary in solution. Since many NIR cyanine dyes have been found to aggregate heavily in aqueous environments, we also evaluated films of these materials to analyze the effect of counter ion on aggregation state and emission intensity from the condensed state. 


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