Dimeric Structure Research Articles

4-amino-5-(pyridin-4-yl)-4H-1,2,4-triazole-3-thiol as potent antimicrobial agent: Synthesis, X-ray, antimicrobial activity and computational studies

In this work, 1,2,4-triazole derivative derived from Isoniazid namely, 4-amino-5-(pyridin-4-yl)-4H-1,2,4-triazole-3-thiol (APTT) was synthesized and fully characterized by FT-IR, 1H NMR, 13C NMR, HRMS-ESI, and single crystal X-ray diffraction. The optimized structures of monomer, dimer and tetramer of APTT with the hybrid B3LYP/6-311++G** method explain the inter and intra-molecular interactions observed experimentally by X-ray diffraction. The presence of tetramer justify the strong IR bands observed in the 2400 and 1800 cm-1 region. The IR spectrum was completely assigned and the scaled force constants reported by using the scaled quantum mechanical force field (SQMFF) approach and the Molvib program. Good correlations between experimental and predicted NMR and UV-Vis spectra are obtained. Both NBO and AIM calculations reveal the inter and intra-molecular interactions and the low stability of APTT in solution while the gap values suggest its low reactivity in the same medium. The different studies reveal the important role of intra and inter-molecular interactions in the stability and reactivity of APTT in the two media. Also, antimicrobial activity of APTT was evaluated against common bacteria and fungi as S. aureus, S. pyrogenes, E. faecalis, V. parahaemolyticus, P. aeruginosa, S. enteritidis, S. cerevisiae, C. albicans, C. tropicalis, C. glabrata, and C. parasilosis. The antimicrobial activity results showed that APTT exhibited both bactericidal and fungicidal activity against all the microbial strains tested. These two effects underline the versatility of the title compound in combating a broad spectrum of microbial infections.

MIPDS: a comprehensive database on the molecular interactions in protein dimer structures

Although many studies have addressed the significance of interactions in the dimeric structures of proteins, there is no dedicated database of these interactions. To this end, the Molecular Interactions in Protein Dimer Structure (MIPDS) database has been developed; it is an open-access repository containing 60 298 3D structures of dimeric proteins sourced from the Protein Data Bank. This helps researchers comprehend the types of interaction, which include those mediated by water, small molecules or ligands and direct interactions, in 3D structures at the molecular level. The database is accessible through a user-friendly interface, where users can conduct searches based on PDB accession number, interaction type and geometric parameters. It can be viewed in textual and graphical formats using the plug-in JSmol. MIPDS is updated weekly using programmed scripts to incorporate newly released dimeric structures and analyses of their interaction types. The database is intended for the scientific community working in structural biology, structural bioinformatics, drug discovery and development. MIPDS is freely accessible to users worldwide at http://dicsoft1.physics.iisc.ac.in/mipds.

Synthesis and Characterization of Copper(II) and Nickel(II) Complexes with 3-(Morpholin-4-yl)propane-2,3-dione 4-Allylthiosemicarbazone Exploring the Antibacterial, Antifungal and Antiradical Properties.

The eleven new copper(II) and nickel(II) coordination compounds [Cu(L)Br]2 (1), [Cu(L)Cl] (2), [Cu(L)NO3] (3), [Ni(L)Cl] (4), [Ni(HL)2](NO3)2 (5), and [Cu(A)(L)]NO3, where A is 1,10-phenanthroline (6), 2,2'-bipyridine (7), 3,4-dimethylpyridine (8), 3-methylpyridine (9), pyridine (10) and imidazole (11) were synthesized with 3-(morpholin-4-yl)propane-2,3-dione 4-allylthiosemicarbazone (HL). The new thiosemicarbazone was characterized by NMR and FTIR spectroscopy. All the coordination compounds were characterized by elemental analysis and FTIR spectroscopy. Also, the crystal structures of HL and complexes 1, 6, 7, and 11 were determined using single-crystal X-ray diffraction analysis. Complex 1 has a dimeric molecular structure with two bromide bridging ligands, while 6, 7, and 11 are ionic compounds and comprise monomeric complex cations. The studied complexes manifest antibacterial and antifungal activities and also have an antiradical activity that, in many cases, surpasses the activity of trolox, which is used as a standard antioxidant in medicine. Copper complexes 1-3 have very weak antiradical properties (IC50 > 100 µM), but nickel complexes 4-5 are strong antiradicals with IC50 values lower than that of trolox. The mixed ligand copper complexes with additional ligand of N-heteroaromatic base are superior to complexes without these additional ligands. They are 1.4-5 times more active than trolox.

Cryo-EM reconstruction of oleate hydratase bound to a phospholipid membrane bilayer

Oleate hydratase (OhyA) is a bacterial peripheral membrane protein that catalyzes FAD-dependent water addition to membrane bilayer-embedded unsaturated fatty acids. The opportunistic pathogen Staphylococcus aureus uses OhyA to counteract the innate immune system and support colonization. Many Gram-positive and Gram-negative bacteria in the microbiome also encode OhyA. OhyA is a dimeric flavoenzyme whose carboxy terminus is identified as the membrane binding domain; however, understanding how OhyA binds to cellular membranes is not complete until the membrane-bound structure has been elucidated. All available OhyA structures depict the solution state of the protein outside its functional environment. Here, we employ liposomes to solve the cryo-electron microscopy structure of the functional unit: the OhyA•membrane complex. The protein maintains its structure upon membrane binding and slightly alters the curvature of the liposome surface. OhyA preferentially associates with 20–30 nm liposomes with multiple copies of OhyA dimers assembling on the liposome surface resulting in the formation of higher-order oligomers. Dimer assembly is cooperative and extends along a formed ridge of the liposome. We also solved an OhyA dimer of dimers structure that recapitulates the intermolecular interactions that stabilize the dimer assembly on the membrane bilayer as well as the crystal contacts in the lattice of the OhyA crystal structure. Our work enables visualization of the molecular trajectory of membrane binding for this important interfacial enzyme.

Lighting Up Bispyrene‐Functionalized Chiral Molecular Muscles with Switchable Circularly Polarized Excimer Emissions

Aiming at the further extension of the application scope of traditional molecular muscles, a novel bispyrene‐functionalized chiral molecular [c2]daisy chain was designed and synthesized. Taking advantage of the unique dimeric interlocked structure of molecular [c2]daisy chain, the resultant chiral molecular muscle emits strong circularly polarized luminescence (CPL) attributed to the pyrene excimer with a high dissymmetry factor (glum) value of 0.010. More importantly, along with the solvent‐ or anion‐ induced motions of the chiral molecular muscle, the precise regulation of the pyrene stacking within its skeleton results in the switching towards either "inversed" state with sign inversion and larger glum values or "down" state with maintained handedness and smaller glum values, making it a novel multistate CPL switch. As the first example of chiral molecular muscle‐based CPL switch, this proof‐of‐concept study not only successfully widens the application scopes of molecular muscles, but also provides a promising platform for the construction of novel smart chiral luminescent materials for practical applications.

Thiazole Functionalization of Thiosemicarbazone for Cu(II) Complexation: Moving toward Highly Efficient Anticancer Drugs with Promising Oral Bioavailability.

In this work, we report the synthesis of a new thiosemicarbazone-based drug of N'-(di(pyridin-2-yl)methylene)-4-(thiazol-2-yl)piperazine-1-carbothiohydrazide (HL) featuring a thiazole spectator for efficient coordination with Cu(II) to give [CuCl(L)]2 (1) and [Cu(NO3)(L)]2 (2). Both 1 and 2 exhibit dimeric structures ascribed to the presence of di-2-pyridylketone moieties that demonstrate dual functions of chelation and intermolecular bridging. HL, 1, and 2 are highly toxic against hepatocellular carcinoma cell lines Hep-G2, PLC/PRF/5, and HuH-7 with half maximal inhibitory concentration (IC50) values as low as 3.26 nmol/mL (HL), 2.18 nmol/mL (1), and 2.54 × 10-5 nmol/mL (2) for PLC/PRF/5. While the free ligand HL may elicit its anticancer effect via the sequestration of bio-relevant metal ions (i.e., Fe3+ and Cu2+), 1 and 2 are also capable of generating cytotoxic reactive oxygen species (ROS) to inhibit cancer cell proliferation. Our preliminary pharmacokinetic studies revealed that oral administration (per os, PO) of HL has a significantly longer half-life t1/2 of 21.61 ± 9.4 h, nearly doubled as compared with that of the intravenous (i.v.) administration of 11.88 ± 1.66 h, certifying HL as an effective chemotherapeutic drug via PO administration.

Drosophila Protein Z4 Possesses ZAD Dimerization Domain.

The transcription factor Z4 (putzig) is one of the key proteins that determine the chromatin structure in Drosophila. Z4 is found at the boundaries of bands on polytene chromosomes, and the bands are currently thought to correlate with chromatin domains. Z4 is a component of a protein complex that additionally includes Chromator and BEAF-32, and a conserved domain is necessary to occur at the N end of Z4 to ensure its interaction with the two proteins. In this study, a zinc finger-associated domain (ZAD) domain was identified in Z4. The capability of dimerization was confirmed for the domain by biochemical methods. A dimer model of the domain was obtained using AlphaFold2, and the model structure was confirmed using small-angle X-ray scattering (SAXS). The dimer structure shows a fold typical of ZAD domains.

TSH Receptor Oligomers Associated With the TSH Receptor Antibody Reactome.

The TSH receptor (TSHR) and its many forms are the primary antigens of Graves' disease as evidenced by the presence of TSHR antibodies of differing biological activity. The TSH holoreceptor undergoes complex posttranslational changes including cleavage of its ectodomain and oligomer formation. We have previously shown that the TSHR exists in both monomeric and dimeric structures in the thyroid cell membrane and have demonstrated, by modeling, that the transmembrane domains (TMD) can form stable dimeric structures. Based on these earlier simulations of the TSHR-TMD structure and our most recent model of the full-length TSHR, we have now built models of full-length TSHR multimers with and without TSH ligand in addition to multimers of the extracellular leucine-rich domain, the site of TSH and autoantibody binding. Starting from these models we ran molecular dynamics simulations of the receptor oligomers solvated with water and counterions; the full-length oligomers also were embedded in a dipalmitoylphosphatidylcholine bilayer. The full-length TSHR dimer and trimer models stayed in the same relative orientation and distance during 2000 ns (or longer) molecular dynamics simulation in keeping with our earlier report of TMD dimerization. Simulations were also performed to model oligomers of the leucine-rich domain alone; we found a trimeric complex to be even more stable than the dimers. These data provide further evidence that different forms of the TSHR add to the complexity of the immune response to this antigen that, in patients with autoimmune thyroid disease, generate an autoantibody reactome with multiple types of autoantibody to the TSHR.

Identifying Target Molecule and Trace Amount of the Byproduct by Two-Dimensional Self-Assembly with Different Solution Concentrations.

Scanning tunneling microscopy (STM) is a powerful way to realize the recognition of self-assembled nanostructures on the atomic scale. In this article, dihexadecyl 6,9-bis((4-(hexadecyloxy)phenyl)ethynyl) phenanthro[9,10-c]thiophene-1,3-dicarboxylate (D-PT) and dihexadecyl 6-bromo-9-((4-(hexadecyloxy) phenyl)ethynyl)phenanthrol[9,10-c]thiophene-1,3-dicarboxylate (S-BrPT) with different substituents were chosen as the target system. D-PT with four side chains as the target molecule and S-BrPT with three side chains and a bromine substituent as the byproduct were mixed in a molar concentration ratio of 20:1. The effect of solution concentration on the molecular self-assembly of the mixture was investigated by STM at the hexadecane/HOPG interface. At high concentrations, only D-PT molecules formed a dimer pattern resulting from the intermolecular van der Waals force and self-adaption. Further diluting the solution, D-PT formed the coexisting dimer and linear structures, in which the linear pattern was formed via solvent coadsorption. At low concentrations, S-BrPT molecules forming N-shaped dimers appeared and filled the linear structure fabricated by D-PT molecules. With further decrease in the concentration, S-BrPT molecules formed N-shaped dimers covering almost half of the surface area, resulting from the C-Br···π and Br···H-C bonds. At very low concentrations, S-BrPT molecules formed N-shaped dimers to arrange the matrix architecture due to the coadsorption of more hexadecane molecules. Density functional theory (DFT) calculations demonstrated that the stronger intermolecular C-Br···π and Br···H-C bonds were significant factors in determining the formation of N-shaped dimers and the stability of this nanostructure. This work enriches the diversity of self-assembled motifs and provides a strategy to characterize different symmetric molecules with trace amounts in a mixed system by STM.

Robust G‐Quadruplex Dimer‐Guided Transmembrane DNA Nanovehicles for Targeted Payload Delivery

Here we report a robust G‐quadruplex (G4) dimer‐guided transmembrane DNA nanovehicle for targeted payload delivery, based on dimeric G4‐proximized aptamers that efficiently target transferrin receptors (TfR) over‐expressed on cancer cell surface. A monomolecular G4 (mono‐G4) named 93del that stably forms the interlocked dimeric structure is employed as the controlling module, which responds to environmental K+ and thereby holds two TfR aptamers at the proximity state. It endows the designed DNA system with over 3‐fold enhancement in cellular internalization, enabling the cancer‐specific delivery of fluorescent G4 ligands and therapeutic drugs for cellular imaging and treatment.

Cryo-EM structures of a bathy phytochrome histidine kinase reveal a unique light-dependent activation mechanism

Phytochromes are photoreceptor proteins in plants, fungi, and bacteria. They can adopt two photochromic states with differential biochemical responses. The structural changes transducing the signal from the chromophore to the biochemical output modules are poorly understood due to challenges in capturing structures of the dynamic, full-length protein. Here, we present cryoelectron microscopy (cryo-EM) structures of the phytochrome from Pseudomonas aeruginosa (PaBphP) in its resting (Pfr) and photoactivated (Pr) state. The kinase-active Pr state has an asymmetric, dimeric structure, whereas the kinase-inactive Pfr state opens up. This behavior is different from other known phytochromes and we explain it with the unusually short connection between the photosensory and output modules. Multiple sequence alignment of this region suggests evolutionary optimization for different modes of signal transduction in sensor proteins. The results establish a new mechanism for light-sensing by phytochrome histidine kinases and provide input for the design of optogenetic phytochrome variants.

The Chemical Bond at the Bottom of the Periodic Table: The Case of the Heavy Astatine and the Super-Heavy Tennessine.

In this work, we study the chemical bond in molecules containing heavy and super-heavy elements according to the current state-of-the-art bonding models. An Energy Decomposition Analysis in combination with Natural Orbital for Chemical Valence (EDA-NOCV) within the relativistic four-component Dirac-Kohn-Sham (DKS) framework is employed, which allows to successfully include the spin-orbit coupling (SOC) effects on the chemical bond description. Simple halogen-bonded adducts ClX⋯L (X=At, Ts; L=NH3, Br-, H2O, CO) of astatine and tennessine have been selected to assess a trend on descending along a group, while modulating the ClX⋯L bond features through the different electronic nature of the ligand L. Interesting effects caused by SOC have been revealed: i) a huge increase of the ClTs dipole moment (which is almost twice as that of ClAt), ii) a lowering of the ClX⋯L bonding energy arising from different contributions to the ClX…L interaction energy strongly depending on the nature of L, iii) a quenching of one of the π back-donation components to the bond. In the ClTs(CO) adduct, the back-donation from ClTs to CO becomes the most important component. The analysis of the electronic structure of the ClX dimers allows for a clear interpretation of the SOC effects in these systems.

Synthesis and Characterization of Alkali Metal Hypersilyl Borates

AbstractThis study focuses on the synthesis of H‐ and MeO‐ functionalized alkali metal hypersilyl borates. Consequently, two distinct silanides were used as polysilane frameworks for our chemical manipulations. Tris(silyl)silanide (1) and tris(trimethoxysilyl)silanide (2) react in the same manner with the BH3 ⋅ SMe2 complex to obtain two new alkali metal hypersilyl borates [(R3Si)3SiBH3M (M=alkali metal; R=H, (3), R=MeO, (4 a–c))] in good to excellent yields. NMR spectroscopy for all compounds and single‐crystal X‐ray crystallography for 3 and 4 a, b enabled a clear structural characterization. Single crystal X‐ray analysis of 3 showed a dimeric structure, where two THF‐molecules and three hydrides from the BH3‐group contribute to the coordination sphere of the lithium atom. Interestingly, crystals suitable for X‐ray analysis of 4 a and 4 b showed a solvent‐free cluster formation, due to the coordination of the MeO groups. Both species form coordination polymers with different coordination modes depending on the nature of the alkali metal. Attempted hydride abstraction reactions of 3 and 4 with various reagents under the formation of the free boranes proceeded unselectively.

Structural Characterization of Disulfide-Linked p53-Derived Peptide Dimers.

Disulfide bonds provide a convenient method for chemoselective alteration of peptide and protein structure and function. We previously reported that mild oxidation of a p53-derived bisthiol peptide (CTFANLWRLLAQNC) under dilute non-denaturing conditions led to unexpected disulfide-linked dimers as the exclusive product. The dimers were antiparallel, significantly α-helical, resistant to protease degradation, and easily reduced back to the original bisthiol peptide. Here we examine the intrinsic factors influencing peptide dimerization using a combination of amino acid substitution, circular dichroism (CD) spectroscopy, and X-ray crystallography. CD analysis of peptide variants suggests critical roles for Leu6 and Leu10 in the formation of stable disulfide-linked dimers. The 1.0 Å resolution crystal structure of the peptide dimer supports these data, revealing a leucine-rich LxxLL dimer interface with canonical knobs-into-holes packing. Two levels of higher-order oligomerization are also observed in the crystal: an antiparallel "dimer of dimers" mediated by Phe3 and Trp7 residues in the asymmetric unit and a tetramer of dimers mediated by Trp7 and Leu10. In CD spectra of Trp-containing peptide variants, minima at 227 nm provide evidence for the dimer of dimers in dilute aqueous solution. Importantly, and in contrast to the original dimer model, the canonical leucine-rich core and robust dimerization of most peptide variants suggests a tunable molecular architecture to target various proteins and evaluate how folding and oligomerization impact various properties, such as cell permeability.

Aggregation of N-Heteropolycyclic Aromatic Molecules: The Acridine Dimer and Trimer.

Polycyclic aromatic hydrocarbons and their nitrogen-substituted analogues are of great interest for various applications in organic electronics. The performance of such devices is determined not only by the properties of the single molecules, but also by the structure of their aggregates, which often form via self-aggregation. Gaining insight into such aggregation processes is a challenging task, but crucial for a fine-tuning of the materials properties. In this work, an efficient approach for the generation and characterisation of aggregates is described, based on matrix-isolation experiments and quantum-chemical calculations. This approach is exemplified for aggregation of acridine. The acridine dimer and trimer are thoroughly analysed on the basis of experimental and calculated UV and IR absorption spectra, which agree well with each other. Thereby a novel structure of the acridine dimer is found, which disagrees with a previously reported one. The calculations also show the changes from excitonic coupling towards orbital interactions between two molecules with decreasing distance to each other. In addition, a structure of the trimer is determined. Finally, an outlook is given on how even higher aggregates can be made accessible through experiment.

Vison condensation and spinon confinement in a kagome-lattice Z2 spin liquid: A numerical study of a quantum dimer model

Quantum spin liquids are exotic many-body states featured with long-range entanglement and fractional anyon quasiparticles. Quantum phase transitions of spin liquids are particularly interesting problems related with novel phenomena of anyon condensation and anyon confinement. Here we study a quantum dimer model, which implements a transition between a Z2 spin liquid (Z2SL) and a valence bond solid (VBS) on the kagome lattice. The transition is driven by the condensation of vison excitation of the Z2 spin liquid, which impacts on other anyon excitations especially leading to the confinement of spinon excitations. By numerical exact diagonalization of the dimer model, we directly measure the vison condensation using vison string operators, and explicitly check a confining potential acting on spinon excitations in the VBS state. It is observed that topological degeneracy of the spin-liquid state is lifted concomitantly with the vison condensation. The dimer ordering pattern of the VBS state is identified by investigating dimer structure factor. Furthermore, we find an interesting state that exhibits features of spin liquid and VBS simultaneously. We discuss the origin of the mixed behaviors and possible scenarios expected in thermodynamic limit. This work complements the previous analytical studies on the dimer model [ and ] by providing numerical evidences on the vison condensation and the spinon confinement in the Z2SL-to-VBS transition. Published by the American Physical Society 2024

Structural Characterization of Pyruvic Acid Dimers Formed inside Helium Nanodroplets by Infrared Spectroscopy and Ab Initio Study.

The structural arrangements of α-keto acid complexes hold significant interest across various fields of chemistry such as enzyme modeling, drug design, or polymer blending. Herein, we report mass-selective infrared (IR) spectra of pyruvic acid monomers and dimers in the range 1720-1820 cm-1 recorded in helium nanodroplets at 0.37 K. The monomer features IR bands at 1807.1 and 1734.5 cm-1, which are assigned to the carboxylic and ketonic C═O stretching vibrations, respectively. Furthermore, the pyruvic acid dimers generated inside the helium nanodroplets are characterized by carboxylic and ketonic C═O stretch vibrations appearing at 1799.2 and 1737.0 cm-1, respectively. This frequency shift of ±7 cm-1 for both C═O stretching bands from the monomer to the dimer demonstrates that the structural motif of the monomer is maintained upon dimer aggregation in helium nanodroplets. The structural assignments were supported by a comparison of the MP2/aug-cc-pVDZ-predicted harmonic vibrational spectra at the C═O stretching region with the experiments. The global minimum monomer structure with an intramolecular hydrogen bond and its dimer stabilized by both inter- and intramolecular hydrogen bonding interactions reproduce the experimental spectra from the monomer and dimer. This assigned dimer structure lies ca.11 kJ/mol above the corresponding global minimum and is favored in helium nanodroplets due to the long-range realignment of molecules via dipole-dipole interaction, followed by short-range stabilization upon intermolecular hydrogen bond formation. The barrier for reconfiguration of the precooled monomer conformer leading to the formation of the most stable dimer structure is around 58 kJ/mol, which is infeasible at 0.37 K.

Spatially asymmetrical copper dimer in ceria as an efficiently synergistic oxidation catalyst

Accurate and facile construction of atomically dispersed active sites is fundamentally important in heterogeneous catalysis. Herein, by applying a unique H2-He pretreatment, we successfully synthesize spatially asymmetrical dimeric Cu stabilized by CeO2. Integrated microscopic and spectroscopic characterizations, together with DFT calculations have revealed the redispersion of Cu species on CeO2 support is accompanied by the formation of Cu dimers with one Cu atom embedded into CeO2 lattice and the neighboring Cu atom supported on-top. The obtained dual-Cu atom catalyst demonstrates its general applicability in emission control scenarios or hydrogen fuel cell for automobile applications with excellent performances. Ab initio calculations reveal that such dimeric Cu sites on CeO2 promote reactant adsorption and lattice oxygen activation, owing to the synergistic effect of unique dimeric Cu structure. This work highlights the great potential of gas pretreatment in the fabrication of dual-atom catalysts, which is widely applicable to active site modulation in advanced oxidation catalysts.

Impact of the spatial structure of alkyl chains on properties of thiophene-substituted diketopyrrolopyrroles: Part II – Spectroscopic study

The study concerns the impact of a difference in geometry of the side alkyl chains of oligothiophene derivatives of diketopyrrolopyrrole (DPP) on their spectroscopic properties and aggregation in solutions, in Langmuir layers, and thin films. Using a combination of theoretical and experimental approaches, this study aims to explain the aggregating behaviour of thiophene-substituted DPP derivatives. Various methods were used to characterise the dyes, including absorption spectroscopy also with polarized light, fluorescence spectroscopy, Langmuir techniques, and time-dependent density functional theory (TD-DFT) calculations. The presented results emphasise a significant impact of side alkyl chains on DPP's molecular behaviour, notably evident in thin-layer structures. Interestingly, the deconvolution of the absorption spectra revealed three bands in the red region. Insightful analysis of temperature-dependent absorption, excitation, and emission fluorescence spectra indicates the co-existence of monomer, dimer, and a higher aggregate forms, most likely a tetrameric structures. Moreover, such a complexity of molecular organisation of dyes appears already in the solution. Differences in spectral properties of the dyes studied are robustly visible in changes in the spectra of the air–water interface, where the dye with the branched side group changes the mutual orientation in dimeric structures, leading to the formation of H-type aggregates, which was observed as an almost 20-nm spectral blue shift during Langmuir layer compression. The results presented highlight the need for care in interpretation of the intensity ratio of DPP spectra and spectral shift as the sole determinants of the aggregation state.

Synthesis, structure and characterization of two new silver-iron based phosphates AgFe2(PO4)2F(H2O)2 and Ag3Fe2(PO4)(HPO4)3

Two new silver-iron based phosphates AgFe2(PO4)2F(H2O)2 (1) with monoclinic P21/n and Ag3Fe2(PO4)(HPO4)3 (2) with triclinic P-1 were synthesized by a conventional hydrothermal method, featuring a dimer structure and a twisted honeycomb-like lattice, respectively. XPS and BVS (Bond Valence Sum) calculations indicated only Fe3+ ions in both compounds, while FT-IR spectra proved the presence of [H2O] in 1 and [OH] groups in 2. Solid-state UV–vis–NIR diffuse reflectance spectra suggested their wide optical band gaps of 2.31 eV and 1.94 eV, respectively. Magnetic measurements indicated that both compounds display a long-range antiferromagnetic ordering at low temperature, showing the change of magnetic entropy of 9.59 J mol−1 K−1 in 1 and that of 14.87 J mol−1 K−1 in 2, respectively.