Types Of Hydrogen Bonds Research Articles

Hydrogen Bonds and FTIR Peaks of Polyether Polyurethane-Urea

Various types of hydrogen bonds exist in polyether polyurethane, polyurethane-urea and polyurea (PUA) and can cause microphase separation. The morphology, properties and applications of polyether PUA are determined by the microphase separation. All kinds of hydrogen bonds make it difficult to assignments of Fourier transform infrared spectroscopy (FTIR) peaks of ether linkage, amine and carbonyl group. This affects the calculation of the hydrogen bonding degree of the hard segments for estimating the degree of microphase separation. This paper summarized hydrogen bonding structures between proton donors and proton acceptors. By analyzing the influence of electronic effect, steric effect, various types of hydrogen bonds and the degree of order of hydrogen bonding on infrared peaks, the relationships between hydrogen bonding structures and infrared peaks are established. Lay the theoretical foundation for evaluating the degree of microphase separation by FTIR method.

A Comparative Study on Properties of Cellulose/Antarctic Krill Protein Composite Fiber by Centrifugal Spinning and Wet Spinning

Cellulose/antarctic krill protein (C/AKP) composite fibers are successfully prepared by centrifugal spinning. The main purpose of this paper is to compare the properties of C/AKP composite fibers prepared by centrifugal spinning and wet spinning. The hydrogen bond type, break strength, morphology, crystallinity, and thermal stability are analyzed by Fourier transform infrared spectroscopy, electronic single silk strength testing, X-ray diffraction, scanning electron microscopy, and differential scanning calorimetry. The results show that the C/AKP composite fibers contain intramolecular hydrogen bonds (OH-OH and annular polymer bonds) and intermolecular hydrogen bonds (OH-π, OH-ether O, and OH-N). The centrifugal spinning composite fibers have a higher percentage of intermolecular hydrogen bonds, a higher break strength, and higher crystallinity than the wet spinning fibers. The wet spinning composite fibers have a more obvious groove structure and a higher degree of swelling than the centrifugally spun fibers.

Synthesis, crystal structure, physicochemical characterization, and dielectric properties of a new organic chloride salt, (C3H7N6)Cl•0.5H2O

The crystallization of (C3H7N6)Cl•0.5H2O is made by slow evaporation at room temperature. It was found to crystallize in the monoclinic system, C2/m space group, with the following lattice parameters: a = 12.4124 (5) A, b = 17.6339 (7) A, c = 7.1193 (3) A, β = 115.057 (2)°, Z = 4, and V = 1411.61 (10) A3. The cohesion in (C3H7N6)Cl•0.5H2O is provided by three types of hydrogen bonds, O–H…Cl, N–H…O, N–H…Cl, and N–H… N. Furthermore, the room temperature IR and Raman spectra of the title compound were recorded and analyzed on the basis of literature data. The optical study was also investigated by UV-Vis absorption. The differential scanning calorimetric (DSC) and dielectric study of this compound has been measured. The percentages of hydrogen bonding interactions are analyzed by fingerprint plots of Hirshfeld surface.

The Double-Faced Nature of Hydrogen Bonding in Hydroxy-Functionalized Ionic Liquids Shown by Neutron Diffraction and Molecular Dynamics Simulations.

We characterize the double-faced nature of hydrogen bonding in hydroxy-functionalized ionic liquids by means of neutron diffraction with isotopic substitution (NDIS), molecular dynamics (MD) simulations, and quantum chemical calculations. NDIS data are fit using the empirical potential structure refinement technique (EPSR) to elucidate the nearest neighbor H⋅⋅⋅O and O⋅⋅⋅O pair distribution functions for hydrogen bonds between ions of opposite charge and the same charge. Despite the presence of repulsive Coulomb forces, the cation-cation interaction is stronger than the cation-anion interaction. We compare the hydrogen-bond geometries of both "doubly charged hydrogen bonds" with those reported for molecular liquids, such as water and alcohols. In combination, the NDIS measurements and MD simulations reveal the subtle balance between the two types of hydrogen bonds: The small transition enthalpy suggests that the elusive like-charge attraction is almost competitive with conventional ion-pair formation.

Docking-based inverse virtual screening strategy for identification of novel protein targets for triclosan

Triclosan (TCS) is chemically designated as 5-chloro-2-(2,4-dichlorophenoxy) phenol and is considered as endocrine-disrupting chemical (EDC). The various diseases found due to exposure of TCS, have been linked with modulation of the human enoyl-acyl carrier protein-reductase (hER). However, the new protein targets for TCS other than hER, which are responsible for various diseases, are still unknown. In the present study, a bioinformatics approach was used to identify new possible targets for TCS. A text mining study was initially performed to understand the association of TCS in various biochemical processes. Discovery studio software 4.1 was used to carry out inverse virtual screening for 226 numbers of pathway proteins by docking study using CHARMm based docking tool, and twenty proteins were screened. CDOCKER energy values lower than −12.65 kcal/mol was considered for the screening of selected proteins. Three new proteins; Receptor-interacting protein 1 (RIP1), Apoptosis signal-regulating kinase 1 (ASK1) and B-cell lymphoma 2 (Bcl-2) from Apoptosis Signaling Pathway revealed best CDOCKER energy with triclosan which was −26.88, −23.34 and −22.96 kcal/mol respectively. The interaction of TCS with RIP1 and ASK1 were mostly hydrophobic; however, hydrogen bond type interaction was found in TCS/Bcl2 complex. Therefore, docking-based inverse virtual screening study suggests that TCS has other targets rather than hER, which can modulate various biochemical processes. The docking protocol was validated through evaluation of root-mean-square deviation (RMSD), key interaction score system (KISS) and the relationship between the docking energy and toxicity data available in ToxCast database. Low RMSD value (0.55 ˚A) and high KISS score (0.66) along with higher correlation (R2 = 0.9798) between docking affinity and toxicity indicated that docking protocol can be used to optimize the binding energetics.

A novel poly (vinyl alcohol)/poly (ethylene glycol) scaffold for tissue engineering with a unique bimodal open-celled structure fabricated using supercritical fluid foaming

In this study, a novel poly (vinyl alcohol) (PVA)/poly (ethylene glycol) (PEG) scaffold was carefully designed via thermal processing and subsequent supercritical fluid (SCF) foaming. Interestingly, a bimodal open-celled structure with interconnected networks was successfully created in the plasticized PVA (WPVA)/PEG scaffold. Large cells were produced from the nucleation sites generated in the PVA phase during rapid depressurization, while plenty of small pores generate in the cell walls of the big cells. The formation mechanism of this cellular structure was studied by considering the various phase morphologies and the diffusion behaviour of the carbon dioxide (CO2) in individual phases. In addition, the intermolecular interactions of the WPVA/PEG blend were studied using X-ray diffraction and FTIR analysis. The results demonstrate that various types of hydrogen bonds among the hydroxyl groups on the PVA chains, PEG and water molecules are formed in the blend system. The realization of thermoplastic foaming of the PVA/PEG blend benefits from the interactions of complexation and plasticization between water and PEG molecules. The SEM images also revealed that L929 fibroblast cells were able to attach and spread on surfaces of the WPVA/PEG samples. Thus the WPVA/PEG scaffold with unique bimodal cellular structure is nontoxic and favours the attachment and proliferation of cells, making it promising for use as the candidate for tissue engineering applications.

Моделирование водородных связей в молекулярных кристаллах тирозина

The problem of the study of hydrogen bonds in biomolecules and living systems is important. Among the drugs, doctors emphasize substances of natural origin involved in metabolic processes. Such compounds include amino acids, peptides, vitamins, enzymes, macro- and microelements, and other biologically active substances, many of which are capable of forming hydrogen bonds. Amino acids and their derivatives are drugs of metabolic pharmacotherapy, characterized by low toxicity and severity of side effects. They also have virtually no allergenic effect, which makes them promising for the creation of drugs or their modifications. The instability of the hydrogen bond can significantly affect the state of pharmaceutical drug containing, for example, amino acids, during their storage, transportation or technological processing. One of the methods for studying the nature and determining the strength of hydrogen bonds is quantum chemical simulation. The calculation of the interaction energy in the studied molecular associate and its decomposition have been carried out according to Morocuma’s method (HF/6-31G (PC GAMESS). The evaluation of such energy components as electrostatic, exchange repulsion, polarization, charge transfer, mixing is given. The main contribution to the interaction energy comes from the electrostatic component. All the studied models have the same distribution of the components of the interaction energy in order of magnitude. Significant difference in the interaction energy in two model systems was noted, that could be explained by different geometry of hydrogen bonds. The comparison of received data made it possible to conclude that there are three types of hydrogen bonds in the molecular tyrosine crystal, which differ from each other in energy and geometry.

Readily Prepared and Tunable Ionic Organocatalysts for Ring-opening Polymerization of Lactones

Highly potent ionic organocatalyst is developed for room-temperature controlled ring-opening polymerization (ROP) of lactones, including δ-valerolactone, ε-caprolactone, and δ-hexalactone. The catalysts are prepared by simply mixing tetra-n-butyl ammonium hydroxide and a (thio)urea at elevated temperature under vacuum, and used in cooperation with an alcoholic initiator. The performance of the catalyst is readily adjusted and optimized through variation of the (thio)urea precursor, catalyst composition, and reaction condition. Urea-derived catalysts are generally superior to thiourea-derived ones. Provided with proper N-substituents, the catalyst affords both high polymerization efficiency and high selectivity for monomer enchainment over macromolecular transesterification, even at high monomer conversion and/or substantially extended reaction time. In addition to acidity, structural symmetry of the urea also proves decisive for the catalytic activity, which enables a catalyst-assisted proton transfer process for the ring-opening of lactone and thus provides a novel mechanistic insight for ROP catalyzed by hydrogen-bonding type bifunctional ionic organocatalysts.

Anisotropy of Thin Foils Obtained from Microwave-Irradiated Poly(Vinyl Alcohol) Aqueous Solutions

In this paper, poly(vinyl alcohol) (PVA) foils of comparable thickness were obtained by using 10 wt % PVA aqueous solutions exposed to microwave (MW) radiations for different times. The main goal of this paper is to identify the effects of MW irradiation on the induced optical birefringence of PVA stretched foils, since it is known that the changes in the chemical and physical properties of polymers induced by radiations can influence the asymmetry of their molecular structures from which the birefringence of polymers derives. The efficiency of the MW oven was estimated, and the contribution of sensible and latent heat and heat loss to the absorbed energy was discussed. The effects of MW irradiation, in terms of absorbed energy, were evidenced by using FTIR spectra analysis, contact angle measurements, scanning electron microscopy (SEM) images, and induced optical birefringence. The dehydration (cross-linking) of PVA in aqueous solution and the dependence of the anisotropy on the absorbed MW energy, stretching ratio, and the type of hydrogen bonds formed are discussed in this study.

Synthesis, crystal structure, photoluminescence, and electroluminescence properties of a new compound containing diphenylmethylene, carbazole, and malononitrile units

Abstract

MECHANOCHEMICAL MODIFICATION OF TRIKLABENDAZOL TO OBTAIN AN EFFECTIVE DRUG AGAINST FACTIOLESIS

To study the possibility of increasing the solubility of the substance triclabendazole (TCB), we used the technology of mechanochemical modification of TCB using water-soluble polymers, polyvinylpyrrolidone (PVP) and arabinogalactan (AG) from Siberian larch Larix sibirica in particular. After joint machining of TCB with polymers (PVP, AG) in a LE-101 ball mill (made in Hungary), free flowing powder dispersions with an increased solubility (more than 50 times as compared to the original substance TCB) were obtained. This result was explained by the formation of intermolecular complexes of the type of hydrogen bond between the characteristic groups of TCB and polymers, which was confirmed by the data of IR-spectral studies. Tests of intermolecular complexes on spontaneously fasciola-infected sheep have shown high efficiency. As a result of the research, it was found that the complex of TCB: AG composition (1:9), which we named “triclafascid”, possesses a number of positive attributes in comparison with the substance of TCB and provides high fasciolocid and economic efficacy, and safety of use by reducing the therapeutic dose. Inclusion of arabinogalactan, which has hepatoprotective, antimutagenic, mitogenic, gastroprotective properties, in the preparation, made it possible to reduce the toxicity of the preparation proposed for practice. It was shown that residual amounts of TCB and its metabolites were not detected in tissues and organs on the 14th day of the experiment with triclafascid, which indicates the possibility of slaughtering an animal and using meat 14 days after using the drug. The drug has good solubility, bioavailability to helminthes, is non-toxic, and increases antihelminthic and economic efficiency. The obtained results confirmed the previously obtained data on the prospects of an innovative approach to improve the quality indicators of anthelmintic drugs and to obtain effective drugs for veterinary medicine.

The cytotoxic effect of Ru(II) complexes with 5-(2-hydroxyphenyl)-3-methyl-1-(2-pyridyl)-1H-pyrazole-4-carboxylic acid methyl ester: Synthesis, X-ray structure and DNA damage potential

A series of arene ruthenium(II) complexes, 1a-3a, with the general formula [(η6-arene)Ru(L)Cl2] (where arene = p-cymene, hexamethylbenzene and benzene, respectively, and L = 5-(2-hydroxyphenyl)-3-methyl-1-(2-pyridyl)-1H-pyrazole-4-carboxylic acid methyl ester) were synthesized and characterized by elemental analysis, MS, IR and 1H NMR spectroscopy. The stability of selected complexes was assessed by UV–Vis spectroscopy over 24 and 48 hour periods. The synthesized complexes were evaluated for in vitro experiments using HL-60, NALM-6, WM-115 and COLO-205, and they showed low cytotoxic activity. The most active compound, 2a, possesses IC50 = 41.17 ± 3.68 µM, which is comparable to the reference compound quercetin. X-ray crystallographic analysis of compound 1a found that the ruthenium complex adopts a piano-stool type of geometry, with crystal packing stabilized by a 3-D net of OH…Cl and CH…Cl type hydrogen bonds, the latter forming dimers in the crystal lattice. The most active complexes in the cytotoxicity experiments were selected for evaluation of the damage percentage in NALM-6 cells by a comet assay: the extent of DNA fragmentation in the lymphoblastic leukemia cells indicated that the analyzed ruthenium(II) complexes triggered DNA damage.

Effects of the inter- and intra-molecular hydrogen bonding interactions in forming atmospheric malonic acid-containing clusters

The possible involvement of chemical compounds in atmospheric new particle formation has received increased attention in recent years. Extensive density functional theory calculations were performed to characterize the effects of the inter- and intra-molecular hydrogen bonding interactions in forming atmospheric malonic acid (MOA)-containing clusters. Methanol, water, formaldehyde, and acetone are common atmospheric nucleation precursors, and they were chosen as the counterpart to interact with MOA. There are two types of hydrogen bonds: addition and insertion. When MOA behaves as the donor of a hydrogen bond, the formation of an inter-molecular hydrogen bond lightly increases the strength of the intra-molecular hydrogen bonds. Strong hydrogen bonds were formed when MOA executes as a hydrogen bond donor. The strength of the insertion conformer depends on the inserting molecule. The IR frequencies of the hydrogen bonded system were investigated. Furthermore, geometrically identified inter- and intra-molecular hydrogen bonds were provided by atoms in molecules approach.

Micellization of poly(2-vinylpyrridine)-b-poly(cyclohexyl methacrylate) (P2VP-b-PCHMA) block copolymers and their interpolymer complex formation in non-aqueous medium

HypothesisThe interpolymer complex formation between poly(vinylpyridine)-based polymers with poly(acrylic acid) (PAA), in aqueous or organic medium, is driven by the hydrogen-bonding complexation. Well-defined nanostructures, with specific practical applications, may be obtained by taking advantage of such non-covalent interactions. ExperimentsPoly(2-vinylpyridine)-b-poly(cyclohexyl methacrylate) (P2VP-b-PCHMA) and poly(2-vinylpyridine)-b-poly(t-butyl methacrylate)-b-poly(cyclohexyl methacrylate) (P2VP-b-PtBuMA-b-PCHMA) copolymers were synthesized by sequential anionic polymerization. Their micellar characteristics were examined as a function of their molecular characteristics in methylcyclohexane and toluene respectively, as cycloaliphatic and aromatic solvents for the selective solubilization of the PCHMA sequence. The size of interpolymer complexes was determined by DLS, in 1,4 dioxane, and their structural composition was characterized by 1H NMR. FindingsThe scaling relationship between the molecular composition and the micellar characteristics, such as particle size and aggregation number, could be established for the PCHMA-based copolymers in methylcyclohexane. It was further demonstrated that controlled micellization in 1,4 dioxane, as a non-selective organic solvent, could be achieved by hydrogen bond type interpolymer complex formation between P2VP-b-PCHMA and PAA-b-PCHMA under stoichiometric P2VP/PAA conditions. Finally, the size of the PCHMA-b-PAA/P2VP block copolymer/homopolymer complexes as well as of the PCHMA-b-PAA/PCHMA-b-P2VP block copolymer/block copolymer complexes was correlated with the molecular characteristics of the copolymers.

Nonbonding interaction analyses on PVDF/[BMIM][BF4] complex system in gas and solution phase.

The present study provides a detailed quantum chemical description of the physicochemical interactions between poly-vinylidene fluoride (PVDF) and 1-butyl-3-methyl-imidazolium tetrafluoro borate ([BMIM][BF4]) ionic liquid (IL). Geometry optimization and frequency calculations are carried out for four monomer units of α- and β-PVDF, [BMIM][BF4], and PVDF/[BMIM][BF4] using dispersion corrected density functional theory. The effects of solvation on the systems under study are demonstrated for three polar aprotic solvents, namely tetra-hydrofuran (THF), acetone, and n,n-dimethyl formamide (DMF) using the integral equation formalism polarizable continuum model (IEFPCM). Calculated negative solvation free energy values suggest solution phase stability of the systems under study. Binding and interaction energies for β-PVDF/IL are found higher in magnitude than those for α-PVDF/IL. The nonbonding interaction phenomenon of β-PVDF/[BMIM][BF4] is elucidated on the basis of natural bond orbital (NBO), Bader's quantum theory of atoms in molecules (QTAIM), delocalization indices, Hirshfeld surface, and reduced density gradient (RDG) analyses. Both anions and cations of ionic liquids are found to show weak van der Waals interaction with PVDF molecule but the anion ([BF4]-)/PVDF interaction is found to be stronger than cation ([BMIM]+)/PVDF interaction. Inter-unit C-H⋯F type hydrogen bonds are found to show improper (causing blue shifts in vibrational frequencies) nature. Frontier molecular orbital analysis is carried out, and different chemical parameters like electronegativity, chemical potential, chemical hardness and softness, and electrophilicity index are calculated using Koopmans' theorem. Thermochemical calculations are also performed, and the variation in different standard thermodynamic parameters with temperature is formulated. Graphical abstract (a) Hirshfeld surface mapped onto electron density and (b) NCI isosurfaces showing inter-unit interactions of β-PVDF/[BMIM][BF4].

Synthesis, crystal structure, infrared spectrum, and thermal properties of [Ni(1,10-phenanthroline)3](fumarate)·9H2O complex with hydrogen bonded supramolecular layers involving fumarate anions

Abstract From the aqueous-ethanolic system Ni(OH)2—H2 fum—phen (H2fum = fumaric acid, phen = 1,10-phenanthroline), novel complex [Ni(phen)3](fum)·9H2O (1) was isolated and characterized by chemical analyses and FT-IR spectroscopy. Results of single crystal X-ray structure analysis have shown that the ionic crystal structure of 1 is built of [Ni(phen)3]2+ complex cations, fumarate dianions and nine crystallographically independent water molecules of crystallization. The Ni(II) atom exhibits hexa-coordination by three phen ligands with mean Ni-N bond length of 2.090 Å. Water molecules form hydrophilic supramolecular layers with fumarate dianions via extended network of O—H···O type hydrogen bonds with O···O distances from the range of 2.676(2)—2. 916(2) Å; hydrophobic complex cations are embedded between these layers. Thermal study of 1 has shown that endothermic dehydration in the temperature range of 95—195 °C takes at least two steps of the process. Graphical Abstract Crystal structure of [Ni(phen)3]fum·9H2O (phen = 1,10-phenanthroline; H2 fum = fumaric acid) which is built of supramolecular layers formed by hydrogen bonded water solvate molecules and fum dianions and between the supramolecular layers embedded [Ni(phen)3]2+ complex cations is described here.

Supramolecular architectures of natural organic matter

A new conceptual model for supramolecular aggregation of natural organic matter (OM) is proposed. Scientific awareness of OM as natural hydrogels is slowly increasing although in the literature they are primarily categorized as physical hydrogels stabilized only by weak interactions. The supramolecular view of OM is here expanded, based on insight from comprehensive hydrogen bond theory, to include three-center–four-electron near-covalent linkages and introduce a new category of metachemical hydrogels that are neither chemical nor physical hydrogels. Hydrogels are typically classified into chemical (permanent, covalently bonded) or physical (reversible, ionic, hydrophobic, or hydrogen bonded) classes based on crosslinking. However, augmented by contemporary advances in hydrogen bonding theory purporting that not all hydrogen bonds are weak and that some hydrogen bonding motifs result in moderate and strong interactions, the popular supramolecular view of OM is extended to include all types of hydrogen bonds. We propose a new category of hydrogels exists—metachemical hydrogels—as a fundamental component of OM. Strong, near covalent, equally shared hydrogel cross-linkages in the metachemical hydrogel can outcompete water. Here, metachemical (≤1 μm diameter) and physical (>1 μm diameter) hydrogels are described as two primary forms of aggregates observed for OM in a hierarchical ‘supramolecular within supramolecular’ self-assembling architecture with new information about shear. The metachemical hydrogels are postulated to be encapsulated within a dispersible physical hydrogel scaffold which can form, dissipate, and spontaneously re-form over turbulent/quiescent cycles indicating reversible abiotic self-assembly. The significance of this investigation is to understand the form OM evolved in nature to provide essential functions. The potential for strong intermolecular forces to form a metachemical hydrogel in OM and the concept of a dynamic dual metachemical/physical hydrogel structure was not previously introduced. The metachemical hydrogel construct should inform hydrogen bonded systems in other chemical and biochemical disciplines.

A novel iron(III) complex: synthesis, spectra, X-ray structure photoluminescence study, and antibacterial properties

The binuclear iron(III) complex of the formula {[Fe(5,5′-dmbpy)2(OH2)]2(µ-O)}(NO3)4 was prepared from the reaction of Fe(NO3)3·9H2O with 5,5′-dimethyl-2,2′-bipyridine. The complex was characterized by FT-IR, UV–Vis, TGA, 1HNMR spectroscopy, elemental analysis, and luminescence measurements. Its structure was investigated using the single-crystal diffraction method. Crystal structure analysis showed that two crystallographically distinct oxygen-bridged Fe(III) cations are each coordinated by two bidentate ligands and one water molecule, resulting in a distorted coordination octahedron formed by four nitrogen atoms and two oxygen atoms. Several types of hydrogen bonds stabilize the crystal packing. In vitro biological screening of the free ligand, the complex and its metal salt against diverse microorganisms was done using the micro-dilution (tube) broth method. The antibacterial effects were also examined in vitro against standard bacterial strains, the Gram-positive Staphylococcus aureus, S. aureus ATCC 25923, and the Gram-negative Escherichia coli; E. coli ATCC 25922. Using these strains, the minimum inhibitory concentration (MIC), minimum bactericidal concentration (MBC) and inhibition zones (IZ) were obtained for the complex, its ligand (5,5′-dmbipy) and its metal salt with Fe(NO3)3.9H2O.

Synthesis and Characterization of 3-(1-((3,4-Dihydroxyphenethyl)amino)ethylidene)-chroman-2,4-dione as a Potential Antitumor Agent.

The newly synthesized coumarin derivative with dopamine, 3-(1-((3,4-dihydroxyphenethyl)amino)ethylidene)-chroman-2,4-dione, was completely structurally characterized by X-ray crystallography. It was shown that several types of hydrogen bonds are present, which additionally stabilize the structure. The compound was tested in vitro against different cell lines, healthy human keratinocyte HaCaT, cervical squamous cell carcinoma SiHa, breast carcinoma MCF7, and hepatocellular carcinoma HepG2. Compared to control, the new derivate showed a stronger effect on both healthy and carcinoma cell lines, with the most prominent effect on the breast carcinoma MCF7 cell line. The molecular docking study, obtained for ten different conformations of the new compound, showed its inhibitory nature against CDKS protein. Lower inhibition constant, relative to one of 4-OH-coumarine, proved stronger and more numerous interactions with CDKS protein. These interactions were carefully examined for both parent molecule and derivative and explained from a structural point of view.

Copper(II) complex with L-arginine – Crystal structure, DFT calculations, spectroscopic, thermal and magnetic properties

Abstract Complex of formula [Cu(L−Arg)(phen)Cl]Cl·2H2O (1) was synthesized in crystalline form (triclinic crystal system, P1 (No. 1) space group with a = 9.376(1) A, b = 10.415(1) A, c = 12.209(2) A and Z = 2). The relations between the crystal structure, DFT calculations, spectroscopic properties (FT−IR, FT−Raman, NIR−Vis−UV, EPR) as well as the parameters of magnetic data were investigated. The square pyramidal geometry around copper (II) cations is very slightly distorted toward bipyramid geometry. The DFT-calculated interaction energies (ΔE) for the L−Arg zwitterion and phen ligands are −135.31 and −54.17 kcal mol−1, respectively. The g tensor diagonal components obey the relationship g|| > g⊥ (g⊥ = 2.063, g|| = 2.23) which suggested the pure dx2-y2 ground state orbital. Analysis of the crystal structure shows two possible magnetic exchange pathways: the neighboring [Cu( l −Arg)(phen)Cl]+ cations are linked in dimeric units by the N−H⋯Cl type hydrogen bonds, and almost parallel phenanthroline molecules provide π–π stacking interaction between the dimers. Analysis of the magnetic data, using an alternating ferro− and antiferromagnetic chain model for S = 1/2 spins, reveals the existence of weak antiferromagnetic coupling within the dimers (JAF = −0.23 cm−1) and weak ferromagnetic interaction between dimers (JF = 0.11 cm−1).