Photochemical Transformations of Peptides Containing the N-(2-Selenoethyl)glycine Moiety

The diselenide bond has attracted considerable attention due to its ability to undergo the metathesis reaction in response to visible light. In our previous study, we demonstrated visible-light-induced diselenide metathesis of selenocysteine-containing linear peptides, allowing for the convenient generation of peptide libraries. Here, we investigated the transformation of linear and cyclic peptides containing the N-(2-selenoethyl)glycine moiety. The linear peptides were highly susceptible to the metathesis reaction, whereas the cyclic systems gave only limited conversion yields of the metathesis product. In both cases, side reactions leading to the formation of mono-, di-, and polyselenides were observed upon prolonged irradiation. To confirm the radical mechanism of the reaction, the radical initiator 2,2'-azobis[2-(2-imidazolin-2-yl)propane] dihydrochloride (VA-044) was tested, and it was found to induce diselenide metathesis without photochemical activation. The data were interpreted in the light of quantum-chemical simulations based on density functional theory (DFT). The simulations were performed at the B3LYP-D3BJ/def2-TZVP level of theory using a continuum solvation model (IEF-PCM) and methanol as a solvent.

Partial Methane Oxidation to Methanol on Ru-Porphyrins - on the Role of Non-Innocent Ligands and Spin Crossover

The partial oxidation reaction of CH4 led to the formation of CH3 OH in the presence of Ru-porphyrin oxo complexes (denoted as POR, POR-O and POR-OH where in the case of the last two, oxygen atom and the OH group were attached to the active site, respectively), in which Ru was present on different oxidation states. The simulations were performed based on Density Functional Theory (DFT) with extended geometric and electronic structure analyses of each reaction step. Moreover, the reaction pathways were investigated in different spin states. The Spin Crossover (SCO) phenomenon was found to play an important role in the kinetics of the reaction in the presence of POR and POR-O. Harmonic Oscillator Model of Aromaticity (HOMA) index was applied for different spin states to estimate the aromaticity changes of the pyrrole rings in the Ru-porphyrin complexes. In order to characterize the nature of bonding, the Natural Bond Orbitals (NBO) analysis including the Wiberg Bond Index (WBI) and Natural Population Analysis (NPA) was carried out. Finally, the Non-Covalent Interactions (NCI) index was employed to gain insight into interactions between the components of the reaction. It was found that the non-covalent interactions cannot be neglected in the studied reaction paths.

Pd and Pt metal atoms as electron donors in σ-hole bonded complexes

Quantum calculations provide a systematic assessment of the ability of Group 10 transition metals M = Pd and Pt to act as an electron donor within the context of pnicogen, chalcogen, and halogen bonds. These M atoms are coordinated in a square planar geometry, attached to two N atoms of a modified phenanthrene unit, as well as two ligand atoms Cl, Br, or I. As the Lewis acid, a series of AFn molecules were chosen, which could form a pnicogen bond (A = P, As, Sb), chalcogen bond (A = S, Se, Te) or halogen bond (A = Cl, Br, I) with M. These noncovalent bonds are fairly strong, varying between 6 and 20 kcal mol-1, with the occupied dz2 orbital of M acting as the origin of charge transferred to the acid. Pt forms somewhat stronger bonds than Pd, and the bond strength rises with the size of the A atom of the acid. Within the context of smaller A atoms, the bond strength rises in the order pnicogen < chalcogen < halogen, but this distinction vanishes for the fifth-row A atoms. The nature of the ligand atoms on M has little bearing on the bond strength. Based on the Harmonic Oscillator Model of Aromaticity (HOMA) index, the ZB, YB and XB bonds were shown to have only a subtle effect on the ring electronic structures.

The Malaprade reaction mechanism for ethylene glycol oxidation by periodic acid based on density functional theory (DFT)

A general mechanism of the Malaprade oxidative carbon-carbon bond cleavage reaction of α-glycol in the presence of periodic acid has been proposed on the basis of density functional theory (DFT) computations. Ethylene glycol and periodic acid, both in their neutral forms, have been studied as noble substrate representatives in model reactions. The proposed reaction mechanism has been constructed based on and compared with previously published experimental kinetic, spectroscopic and temperature and pH-dependent studies. In the presented theoretical mechanistic considerations, four alternative molecular transformations have been analyzed from thermodynamic and kinetic points of view. Theoretically, the predicted activation energy barriers have been compared with experimental ones published elsewhere. The presented minimum energy pathway (MEP) unveiled the shape and conformation of the intermediate and transition state structures. The three-step reaction process involves the formation of a seven-membered quasi-ring assisted by an intramolecular hydrogen-bond intermediate structure forming one I-O bond (IC1_B), a cyclic ester intermediate forming two I-O bonds (IC2_C) and the final products formed at the two very last stages (HIO3, water and two formaldehyde molecules). The computed and energetically the most favourable reaction landscape proposed in this work uniforms and refines the mechanistic proposition given by Criegee for Malaprade type of reactions and further gives a detailed molecular understanding of the reaction rate and atomic connections en route the transformation. The molecular geometries of all stationary points (intermediate and transition state structures) lying on the potential energy hypersurface have been optimized at the four alternative DFT levels under the solvation model based on the density approximation: B3PW91, CAM-B3LYP, BMK, ωB97XD. The 6-311+G(2d,p) basis set for C, O, and H atoms and both the full (DGDZVP) and Ahlrichs-Weigend1 (def2-TZVP) basis sets for iodine atoms were used during the computations.

Heterobimetallic 21,23-dimetallaporphyrin: activation of metal-metal interactions within the porphyrinoid macrocycle

Two core-modified porphyrins containing metal atoms, namely platinum(II) or platinum(IV) and rhodium(III), in place of two NH units, have been obtained by a post-synthetic modification of the 21,23-ditelluraporphyrin. The products of the tellurium-to-metal exchange, 21-platina-23-rhodaporphyrins, incorporate rhodacyclopentadiene and platinacyclopentadiene units with the metal atoms facing each other. The two molecules exhibit different degrees of metal-metal interaction depending on the oxidation state of platinum, with the NBO bond order being 0.04 for platinum(IV) and 0.15 for platinum(II). Consistently, the Quantum Theory of Atoms in Molecules analysis revealed the presence of the bond determinant, the bond critical point, in the platinum(II) species, in contrast to the platinum(IV) congener. The two porphyrinoids are interconvertible in redox reactions. They both exhibit fluxional behaviour in solution, studied by ¹H NMR, involving alteration in the metal ion coordination sphere accompanied by the macrocyclic skeleton conformation change.

Static and Dynamical Quantum Studies of CX3-AlX2 and CSiX3-BX2 (X = F, Cl, Br) Complexes with Hydrocyanic Acid: Unusual Behavior of Strong π-Hole at Triel Center

The set of TX₃-TrX₂ (T = C, Si, Ge; Tr = B, Al, Ga; X = F, Cl, Br) molecules offers a rather unique opportunity to study both σ-hole and π-hole dimerization on the tetrel and triel ends, respectively. According to the molecular electrostatic potential (MEP) distribution, the π-hole extrema (acidic sites) were more intense than their σ-hole counterparts. The molecules owning the most (CX₃-AlX₂) and least (SiX₃-BX₂) intense π-holes were chosen to evaluate their capacities to attract one and two HCN molecules (Lewis bases). We discovered that the energetic characteristics of π-hole dimers severely conflict with the monomers MEP pattern since the weakest π-hole monomer forms a dimer characterized by interaction energy compared to those created by the monomers with noticeably greater power in the π-hole region. This outcome is due to the deformation of the weakest π-hole donor. Furthermore, the MEP analysis for monomers in the geometry of respective dimers revealed a "residual π-hole" site that was able to drive second ligand attachment, giving rise to the two "unusual trimers" examined further by the NCI and QTAIM analyses. Apart from them, the π-hole/π-hole and σ-hole/π-hole trimers have also been obtained throughout this study and described using energetic and geometric parameters. The SAPT approach revealed details of the bonding in one of the "unusual trimers". Finally, Born-Oppenheimer Molecular Dynamics (BOMD) simulations were carried out to investigate the time evolution of the interatomic distances of the studied complexes as well as their stability.

Role of Non-Covalent Interactions in Carbonic Anhydrase I-Topiramate Complex Based on QM/MM Approach

Carbonic anhydrase (CA) I with a Topiramate (TPM) complex was investigated on the basis of a Quantum Mechanics/Molecular Mechanics (QM/MM) approach. The QM part was treated using Density Functional Theory (DFT) while the MM was simulated using Amberff14SB and GAFF force fields. In addition, the TIP3P model was applied to reproduce the polar environment influence on the studied complex. Next, three snapshots (after 5 ps, 10 ps, and 15 ps of the simulation time) were taken from the obtained trajectory to provide an insight into the non-covalent interactions present between the ligand and binding pocket of the protein. Our special attention was devoted to the binding site rearrangement, which is known in the literature concerning the complex. This part of the computations was performed using ωB97X functional with Grimme D3 dispersion corrections as well as a Becke-Johnson damping function (D3-BJ). Two basis sets were applied: def2-SVP (for larger models) and def2-TZVPD (for smaller models), respectively. In order to detect and describe non-covalent interactions between amino acids of the binding pocket and the ligand, Independent Gradient Model based on Hirshfeld partitioning (IGMH), Interaction Region Indicator (IRI), Quantum Theory of Atoms in Molecules (QTAIM) and Natural Bond Orbitals (NBO) methods were employed. Finally, Symmetry-Adapted Perturbation Theory (SAPT) was applied for energy decomposition between the ligand and protein. It was found that during the simulation time, the ligand position in the binding site was preserved. Nonetheless, amino acids interacting with TPM were exchanging during the simulation, thus showing the binding site reorganization. The energy partitioning revealed that dispersion and electrostatics are decisive factors that are responsible for the complex stability.

Inter- vs. Intra-Molecular Hydrogen Bond in Complexes of Nitrophthalic Acids with Pyridine

This study covers the analysis of isomeric forms of nitrophthalic acids with pyridine. This work dwells on the complementary experimental (X-ray, IR and Raman) and theoretical (Car-Parrinello Molecular Dynamics (CPMD) and Density Functional Theory (DFT)) studies of the obtained complexes. The conducted studies showed that steric repulsion between the nitro group in ortho-position and the carboxyl group causes significant isomeric changes. Modeling of the nitrophthalic acid—pyridine complex yielded a short strong intramolecular hydrogen bond (SSHB). The transition energy from the isomeric form with an intermolecular hydrogen bond to the isomeric form with an intramolecular hydrogen bond was estimated.

Affinities to Oxaliplatin: Vitamins from B Group vs. Nucleobases

Oxaliplatin, similar to Cisplatin, exhibits anticancer activity by interacting with DNA and inducing programmed cell death. It is biotransformed through a number of spontaneous and non-enzymatic processes. In this way, several transient reactive species are formed, including dichloro-, monochloro-, and diaqua-DACH platin, which can complex with DNA and other macromolecules. The molecular level suggests that such interactions can also take place with vitamins containing aromatic rings with lone pair orbitals. Theoretical and experimental studies were performed to investigate interactions of vitamins from the B group with Oxaliplatin, and the results were compared with values characterizing native purines. Quantum-chemical simulations were carried out at the B3LYP/6-31G(d,p) level, with the LANL2DZ basis set representing atomic orbitals of platinum atom, and at the MN15/def2-TZVP levels of theory with the use of Polarizable Continuum Model (IEF-PCM formulation) and water as a solvent. Additionally, time-dependent density functional theory (TD-DFT) was employed to study molecular properties in the electronic excited state. Interactions of vitamins and Oxaliplatin were investigated using UV-Vis spectroscopy. Values of the free energy (ΔG_r) indicate spontaneous reactions with monoaqua [PtH₂OClDACH]⁺ and diaqua [Pt(H₂O)₂DACH]²⁺ derivatives of Oxaliplatin. However, diaqua derivatives were found to be preferable. The free energy (ΔG_r) values obtained for vitamins from the B group indicate lower affinity of Oxaliplatin compared with values characterizing complexes formed by guanine, adenine, and cytosine. The exception is the monoaqua form of vitamin B1 (thiamine) at the MN15/def2-TZVP levels of calculations. An application of atoms in molecules (AIM) theory revealed non-covalent interactions present in the complexes studied. The comparison of computed and experimental spectroscopic properties showed a good agreement.

A new mixed-valence CuI/CuII three-dimensional coordination polymer constructed with an N,O-donor ligand generated via solvothermal synthesis: structural features and magnetic properties

A new mixed-valence CuI/CuII three-dimensional coordination polymer, poly[[diaquabis[μ4-2-(pyrazin-2-yl)quinoline-4-carboxylato]dicopper(I)copper(II)] bis(tetrafluoridoborate)], {[Cu3(C14H8N3O2)2(H2O)2](BF4)2} n , was synthesized and characterized, with 2-(pyrazin-2-yl)quinoline-4-carboxylic acid being employed as a linker ligand. The ligand was isolated as its hydrochloride salt, 4-carboxy-2-(pyrazin-2-yl)quinolin-1-ium chloride dihydrate, C14H10N3O2 +·Cl−·2H2O. The compounds show luminescence at 550 nm for the ligand and at 565 nm for the polymer at 297 K. The ligand structure was rationalized by means of quantum-chemical calculations, which led to a similar conformation to that determined from X-ray diffraction studies.

Revealing Intra- and Intermolecular Interactions Determining Physico-Chemical Features of Selected Quinolone Carboxylic Acid Derivatives

The intra- and intermolecular interactions of selected quinolone carboxylic acid derivatives were studied in monomers, dimers and crystals. The investigated compounds are well-recognized as medicines or as bases for further studies in drug design. We employed density functional theory (DFT) in its classical formulation to develop gas-phase and solvent reaction field (PCM) models describing geometric, energetic and electronic structure parameters for monomers and dimers. The electronic structure was investigated based on the atoms in molecules (AIM) and natural bond orbital (NBO) theories. Special attention was devoted to the intramolecular hydrogen bonds (HB) present in the investigated compounds. The characterization of energy components was performed using symmetry-adapted perturbation theory (SAPT). Finally, the time-evolution methods of Car-Parrinello molecular dynamics (CPMD) and path integral molecular dynamics (PIMD) were employed to describe the hydrogen bond dynamics as well as the spectroscopic signatures. The vibrational features of the O-H stretching were studied using Fourier transformation of the autocorrelation function of atomic velocity. The inclusion of quantum nuclear effects provided an accurate depiction of the bridged proton delocalization. The CPMD and PIMD simulations were carried out in the gas and crystalline phases. It was found that the polar environment enhances the strength of the intramolecular hydrogen bonds. The SAPT analysis revealed that the dispersive forces are decisive factors in the intermolecular interactions. In the electronic ground state, the proton-transfer phenomena are not favourable. The CPMD results showed generally that the bridged proton is localized at the donor side, with possible proton-sharing events in the solid-phase simulation of stronger hydrogen bridges. However, the PIMD enabled the quantitative estimation of the quantum effects inclusion-the proton position was moved towards the bridge midpoint, but no qualitative changes were detected. It was found that the interatomic distance between the donor and acceptor atoms was shortened and that the bridged proton was strongly delocalized.

Intermolecular Interactions and Spectroscopic Signatures of the Hydrogen-Bonded System-n-Octanol in Experimental and Theoretical Studies

n-Octanol is the object of experimental and theoretical study of spectroscopic signatures and intermolecular interactions. The FTIR measurements were carried out at 293 K for n-octanol and its deuterated form. Special attention was paid to the vibrational features associated with the O-H stretching and the isotope effect. Density Functional Theory (DFT) in its classical formulations was applied to develop static models describing intermolecular hydrogen bond (HB) and isotope effect in the gas phase and using solvent reaction field reproduced by Polarizable Continuum Model (PCM). The Atoms in Molecules (AIM) theory enabled electronic structure and molecular topology study. The Symmetry-Adapted Perturbation Theory (SAPT) was used for energy decomposition in the dimers of n-octanol. Finally, time-evolution methods, namely classical molecular dynamics (MD) and Car-Parrinello Molecular Dynamics (CPMD) were employed to shed light onto dynamical nature of liquid n-octanol with emphasis put on metric and vibrational features. As a reference, CPMD gas phase results were applied. Nuclear quantum effects were included using Path Integral Molecular Dynamics (PIMD) and a posteriori method by solving vibrational Schrödinger equation. The latter applied procedure allowed to study the deuterium isotope effect.

Exploring Intra- and Intermolecular Interactions in Selected N-Oxides-The Role of Hydrogen Bonds

Intra- and intermolecular interactions have been explored in selected N-oxide derivatives: 2-(N,N-dimethylamino-N-oxymethyl)-4,6-dimethylphenyl (1) and 5,5’-dibromo-3-diethylaminomethyl-2,2’-biphenol N-oxide (2). Both compounds possess intramolecular hydrogen bonding, which is classified as moderate in 1 and strong in 2, and resonance-assisted in both cases. Density Functional Theory (DFT) in its classical formulation as well as Time-Dependent extension (TD-DFT) were employed to study proton transfer phenomena. The simulations were performed in the gas phase and with implicit and explicit solvation models. The obtained structures of the studied N-oxides were compared with experimental data available. The proton reaction path was investigated using scan with an optimization method, and water molecule reorientation in the monohydrate of 1 was found upon the proton scan progress. It was found that spontaneous proton transfer phenomenon cannot occur in the electronic ground state of the compound 1. An opposite situation was noticed for the compound 2. The changes of nucleophilicity and electrophilicity upon the bridged proton migration were analyzed on the basis of Fukui functions in the case of 1. The interaction energy decomposition of dimers and microsolvation models was investigated using Symmetry-Adapted Perturbation Theory (SAPT). The simulations were performed in both phases to introduce polar environment influence on the interaction energies. The SAPT study showed rather minor role of induction in the formation of homodimers. However, it is worth noticing that the same induction term is responsible for the preference of water molecules’ interaction with N-oxide hydrogen bond acceptor atoms in the microsolvation study. The Natural Bond Orbital (NBO) analysis was performed for the complexes with water to investigate the charge flow upon the polar environment introduction. Finally, the TD-DFT was applied for isolated molecules as well as for microsolvation models showing that the presence of solvent affects excited states, especially when the N-oxide acceptor atom is microsolvated.

Biological Evaluation and Molecular Docking Studies of Novel 1,3,4-Oxadiazole Derivatives of 4,6-Dimethyl-2-sulfanylpyridine-3-carboxamide

To date, chronic inflammation is involved in most main human pathologies such as cancer, and autoimmune, cardiovascular or neurodegenerative disorders. Studies suggest that different prostanoids, especially prostaglandin E₂, and their own synthase (cyclooxygenase enzyme-COX) can promote tumor growth by activating signaling pathways which control cell proliferation, migration, apoptosis, and angiogenesis. Non-steroidal anti-inflammatory drugs (NSAIDs) are used, alongside corticosteroids, to treat inflammatory symptoms particularly in all chronic diseases. However, their toxicity from COX inhibition and the suppression of physiologically important prostaglandins limits their use. Therefore, in continuation of our efforts in the development of potent, safe, non-toxic chemopreventive compounds, we report herein the design, synthesis, biological evaluation of new series of Schiff base-type hybrid compounds containing differently substituted N-acyl hydrazone moieties, 1,3,4-oxadiazole ring, and 4,6-dimethylpyridine core. The anti-COX-1/COX-2, antioxidant and anticancer activities were studied. Schiff base 13, containing 2-bromobenzylidene residue inhibited the activity of both isoenzymes, COX-1 and COX-2 at a lower concentration than standard drugs, and its COX-2/COX-1 selectivity ratio was similar to meloxicam. Furthermore, the results of cytotoxicity assay indicated that all of the tested compounds exhibited potent anti-cancer activity against A549, MCF-7, LoVo, and LoVo/Dx cell lines, compared with piroxicam and meloxicam. Moreover, our experimental study was supported by density functional theory (DFT) and molecular docking to describe the binding mode of new structures to cyclooxygenase.

How Substitution Combines with Non-Covalent Interactions to Modulate 1,4-Naphthoquinone and Its Derivatives Molecular Features-Multifactor Studies

Substitution is well-known to modulate the physico-chemical properties of molecules. In this study, a combined, multifactor approach was employed to determine a plethora of substitution patterns using –Br and –O-H in 1,4-naphthoquinone and its derivatives. On the basis of classical Density Functional Theory (DFT), 25 models divided into three groups were developed. The first group contains 1,4-naphthoquinone and its derivatives substituted only by –Br. The second group consists of compounds substituted by –Br and one –O-H group. As a result of the substitution, an intramolecular hydrogen bond was formed. The third group also contains –Br as a substituent, but two –O-H groups were introduced and two intramolecular hydrogen bonds were established. The simulations were performed at the ωB97XD/6-311++G(2d,2p) level of theory. The presence of substituents influenced the electronic structure of the parent compound and its derivatives by inductive effects, but it also affected the geometry of the 2 and 3 groups, due to the intramolecular hydrogen bonding and the formation of a quasi-ring/rings. The static DFT models were applied to investigate the aromaticity changes in the fused rings based on the Harmonic Oscillator Model of Aromaticity (HOMA). The OH stretching was detected for the compounds from groups 2 and 3 and further used to find correlations with energetic parameters. The evolution of the electronic structure was analyzed using Hirshfeld atomic charges and the Substituent Active Region (cSAR) parameter. The proton reaction path was investigated to provide information on the modulation of hydrogen bridge properties by diverse substitution positions on the donor and acceptor sides. Subsequently, Car–Parrinello Molecular Dynamics (CPMD) was carried out in the double-bridged systems (group 3) to assess the cooperative effects in double –O-H-substituted systems. It was determined that the –O-H influence on the core of the molecule is more significant than that of –Br, but the latter has a major impact on the bridge dynamics. The competitive or synergic effect of two –Br substituents was found to depend on the coupling between the intramolecular hydrogen bridges. Thus, the novel mechanism of a secondary (cooperative) substituent effect was established in the double-bridged systems via DFT and CPMD results comparison, consisting of a mediation of the bromine substitutions’ influence by the cooperative proton transfer events in the hydrogen bridges.

Non-Covalent Forces in Naphthazarin-Cooperativity or Competition in the Light of Theoretical Approaches

Non-covalent interactions responsible for molecular features and self-assembly in Naphthazarin C polymorph were investigated on the basis of diverse theoretical approaches: Density Functional Theory (DFT), Diffusion Quantum Monte Carlo (DQMC), Symmetry-Adapted Perturbation Theory (SAPT) and Car-Parrinello Molecular Dynamics (CPMD). The proton reaction paths in the intramolecular hydrogen bridges were studied. Two potential energy minima were found indicating that the proton transfer phenomena occur in the electronic ground state. Diffusion Quantum Monte Carlo (DQMC) and other levels of theory including Coupled Cluster (CC) employment enabled an accurate inspection of Potential Energy Surface (PES) and revealed the energy barrier for the proton transfer. The structure and reactivity evolution associated with the proton transfer were investigated using Harmonic Oscillator Model of Aromaticity - HOMA index, Fukui functions and Atoms In Molecules (AIM) theory. The energy partitioning in the studied dimers was carried out based on Symmetry-Adapted Perturbation Theory (SAPT) indicating that dispersive forces are dominant in the structure stabilization. The CPMD simulations were performed at 60 K and 300 K in vacuo and in the crystalline phase. The temperature influence on the bridged protons dynamics was studied and showed that the proton transfer phenomena were not observed at 60 K, but the frequent events were noticed at 300 K in both studied phases. The spectroscopic signatures derived from the CPMD were computed using Fourier transformation of autocorrelation function of atomic velocity for the whole molecule and bridged protons. The computed gas-phase IR spectra showed two regions with OH absorption that covers frequencies from 2500 cm−1 to 2800 cm−1 at 60 K and from 2350 cm−1 to 3250 cm−1 at 300 K for both bridged protons. In comparison, the solid state computed IR spectra revealed the environmental influence on the vibrational features. For each of them absorption regions were found between 2700–3100 cm−1 and 2400–2850 cm−1 at 60 K and 2300–3300 cm−1 and 2300–3200 cm−1 at 300 K respectively. Therefore, the CPMD study results indicated that there is a cooperation of intramolecular hydrogen bonds in Naphthazarin molecule.

Competition of Intra- and Intermolecular Forces in Anthraquinone and Its Selected Derivatives

Intra- and intermolecular forces competition was investigated in the 9,10-anthraquinone (1) and its derivatives both in vacuo and in the crystalline phase. The 1,8-dihydroxy-9,10-anthraquinone (2) and 1,8-dinitro-4,5-dihydroxy-anthraquinone (3) contain Resonance-Assisted Hydrogen Bonds (RAHBs). The intramolecular hydrogen bonds properties were studied in the electronic ground and excited states employing Møller-Plesset second-order perturbation theory (MP2), Density Functional Theory (DFT) method in its classical formulation as well as its time-dependent extension (TD-DFT). The proton potential functions were obtained via scanning the OH distance and the dihedral angle related to the OH group rotation. The topological analysis was carried out on the basis of theories of Atoms in Molecules (AIM-molecular topology, properties of critical points, AIM charges) and Electron Localization Function (ELF-2D maps showing bonding patterns, calculation of electron populations in the hydrogen bonds). The Symmetry-Adapted Perturbation Theory (SAPT) was applied for the energy decomposition in the dimers. Finally, Car-Parrinello molecular dynamics (CPMD) simulations were performed to shed light onto bridge protons dynamics upon environmental influence. The vibrational features of the OH stretching were revealed using Fourier transformation of the autocorrelation function of atomic velocity. It was found that the presence of OH and NO2 substituents influenced the geometric and electronic structure of the anthraquinone moiety. The AIM and ELF analyses showed that the quantitative differences between hydrogen bonds properties could be neglected. The bridged protons are localized on the donor side in the electronic ground state, but the Excited-State Intramolecular Proton Transfer (ESIPT) was noticed as a result of the TD-DFT calculations. The hierarchy of interactions determined by SAPT method indicated that weak hydrogen bonds play modifying role in the organization of these crystal structures, but primary ordering factor is dispersion. The CPMD crystalline phase results indicated bridged proton-sharing in the compound 2.

Inter- vs. Intramolecular Hydrogen Bond Patterns and Proton Dynamics in Nitrophthalic Acid Associates

Noncovalent interactions are among the main tools of molecular engineering. Rational molecular design requires knowledge about a result of interplay between given structural moieties within a given phase state. We herein report a study of intra- and intermolecular interactions of 3-nitrophthalic and 4-nitrophthalic acids in the gas, liquid, and solid phases. A combination of the Infrared, Raman, Nuclear Magnetic Resonance, and Incoherent Inelastic Neutron Scattering spectroscopies and the Car-Parrinello Molecular Dynamics and Density Functional Theory calculations was used. This integrated approach made it possible to assess the balance of repulsive and attractive intramolecular interactions between adjacent carboxyl groups as well as to study the dependence of this balance on steric confinement and the effect of this balance on intermolecular interactions of the carboxyl groups.

Fluconazole and Lipopeptide Surfactin Interplay During Candida albicans Plasma Membrane and Cell Wall Remodeling Increases Fungal Immune System Exposure

Recognizing the β-glucan component of the Candida albicans cell wall is a necessary step involved in host immune system recognition. Compounds that result in exposed β-glucan recognizable to the immune system could be valuable antifungal drugs. Antifungal development is especially important because fungi are becoming increasingly drug resistant. This study demonstrates that lipopeptide, surfactin, unmasks β-glucan when the C. albicans cells lack ergosterol. This observation also holds when ergosterol is depleted by fluconazole. Surfactin does not enhance the effects of local chitin accumulation in the presence of fluconazole. Expression of the CHS3 gene, encoding a gene product resulting in 80% of cellular chitin, is downregulated. C. albicans exposure to fluconazole changes the composition and structure of the fungal plasma membrane. At the same time, the fungal cell wall is altered and remodeled in a way that makes the fungi susceptible to surfactin. In silico studies show that surfactin can form a complex with β-glucan. Surfactin forms a less stable complex with chitin, which in combination with lowering chitin synthesis, could be a second anti-fungal mechanism of action of this lipopeptide.

New anticandidal Cu(i) complexes with neocuproine and ketoconazole derived diphenyl(aminomethyl)phosphane: luminescence properties for detection in fungal cells

Anticandidal activity and a complex luminescence in water solutions of the new copper(i) complexes with a ketoconazole derived phosphane ligand.

N-oxide Derivatives: Car-Parrinello Molecular Dynamics and Electron Localization Function Study on Intramolecular Hydrogen Bonds

First-principle molecular dynamics simulations (CPMD) and electron localization function (ELF) topological analysis were performed for two N-oxides, 2-[( N, N-dimethylamino- N-oxy)methyl]-4,6-dimethylphenol (I) and 5,5'-dibromo-3-[(diethylamino)methyl]-2,2'-biphenol N-oxide (II). Special attention was paid to hydrogen bond dynamics and spectroscopic features. Simulations were carried out in vacuo and in the crystalline phase. It was found that for compound I proton transfer phenomena do not occur spontaneously. An opposite situation was noticed for one of the two intramolecular hydrogen bonds of compound II. The influence of the neighboring molecules (including microsolvation) and the crystal field on the hydrogen bond properties cannot be neglected. Hydrogen bond spectroscopic signatures were quite well reproduced by power spectra of atomic velocity. Metric and spectroscopic theoretical findings were compared with experimental data available, especially in a view of the fact that experimental X-ray diffraction and FT-IR data of compound II indicate strong delocalization of the N-oxide bridge proton. ELF analysis showed that for compound II the N-oxide bridge belongs to the topological category of strong hydrogen bonds with the separate ELF basin for the bridged hydrogen atom.

A molecular roundabout: triple cyclically arranged hydrogen bonds in light of experiment and theory

This paper dwells on the synthesis and diverse studies of cyclically arranged hydrogen bridges in tris-hydroxy aryl Schiff bases. Experimental (IINS, IR, Raman and X-ray) and theoretical (CPMD, DFTP and DFT) studies of tris-hydroxy aryl Schiff bases have been performed in the solid state.

First-Principle Molecular Dynamics Study of Selected Schiff and Mannich Bases: Application of Two-Dimensional Potential of Mean Force to Systems with Strong Intramolecular Hydrogen Bonds

Car-Parrinello Molecular Dynamics simulations were performed for selected anharmonic systems, i.e., Schiff and Mannich base-type compounds, to investigate the vibrational properties associated with O-H stretching. All calculations were performed in the gas phase to compare them with available experimental data. First the vibrational properties of the two compounds were analyzed on the basis of well-established approaches:  Fourier transformation of the autocorrelation function of both the atomic velocities and dipole moments. Then path integral molecular dynamics simulations were performed to demonstrate the influence of quantum effects on the proton's position in the hydrogen bridge. In addition, quantum effects were incorporated a posteriori into calculations of O-H stretching envelopes for the Schiff and Mannich bases. Proton potential snapshots were extracted from the ab initio molecular dynamics trajectory. Vibrational Schrödinger equations (one- and two-dimensional) were solved numerically for the snapshots, and the O-H stretching envelopes were calculated as a superposition of the 0→1 transitions. Subsequently, one- and two-dimensional potentials of mean force (1D and 2D pmf) were calculated for the proton stretching mode from the proton vibrational eigenfunctions and eigenvalues incorporating statistical sampling and nuclear quantum effects. The results show that the applied methodologies are in good agreement with experimental infrared spectra. Additionally, it is demonstrated that the 2D pmf method could be applied in systems with strong anharmonicity to describe the properties of the O-H stretching mode more accurately. Future applications of the 2D pmf technique include, in principle, large biomolecular systems treated within the QM/MM framework.

Molecular reorganization of selected quinoline derivatives in the ground and excited states—Investigations via static DFT

Quinoline derivatives are interesting objects to study internal reorganizations due to the observed excited-state-induced intramolecular proton transfer (ESIPT). Here, we report on computations for selected 12 quinoline derivatives possessing three kinds of intramolecular hydrogen bonds. Density functional theory was employed for the current investigations. The metric and electronic structure simulations were performed for the ground state and first excited singlet and triplet states. The computed potential energy profiles do not show a spontaneous proton transfer in the ground state, whereas excited states exhibit this phenomenon. Atoms in Molecules (AIM) theory was applied to study the nature of hydrogen bonding, whereas Harmonic Oscillator Model of aromaticity index (HOMA) provided data of aromaticity evolution as a derivative of the bridge proton position. The AIM-based topological analysis confirmed the presence of the intramolecular hydrogen bonding. In addition, using the theory, we were able to provide a quantitative illustration of bonding transformation: from covalent to the hydrogen. On the basis of HOMA analysis, we showed that the aromaticity of both rings is dependent on the location of the bridge proton. Further, the computed results were compared with experimental data available. Finally, ESIPT occurrence was compared for the three investigated kinds of hydrogen bridges, and competition between two bridges in one molecule was studied.

N-H⋯O versus O-H⋯O: density functional calculation and first principle molecular dynamics study on a quinoline-2-carboxamide N-oxide

N-oxide-type compounds are the object of current research interest due to the presence of resonance-assisted N–H⋯O hydrogen bonds. Here, the metric and spectroscopic parameters of N-methyl-quinoline-2-carboxamide 1-oxide were computed on the basis of density functional theory and Car-Parrinello molecular dynamics. Computations were performed in vacuo and in solid state; for both phases additional simulations with Grimme’s dispersion correction were carried out. The approaches used were able to reproduce correctly the structural aspects of the studied compound and shed more light on the hydrogen bonding with special focus on bridge proton mobility. Proton transfer phenomena were found not to occur in the investigated compound, and the bridge proton was localized to the donor site. This observation is in agreement with the classical theory of the acidity of donor–acceptor sites. The presence of hydrogen bonding was confirmed using atoms-in-molecules theory. The computational results were compared with available experimental data.

Counter propagation artificial neural network categorical models for prediction of carcinogenicity for non-congeneric chemicals

One of the main goals of the new chemical regulation REACH (Registration, Evaluation and Authorization of Chemicals) is to fill the gaps on the toxicological properties of chemicals that affect human health. Carcinogenicity is one of the endpoints under consideration. The information obtained from (quantitative) structure-activity relationship ((Q)SAR) models is accepted as an alternative solution to avoid expensive and time-consuming animal tests. The reported results were obtained within the framework of the European project 'Computer Assisted Evaluation of industrial chemical Substances According to Regulations (CAESAR)'. In this article, we demonstrate intermediate results for counter propagation artificial neural network (CP ANN) models for the prediction category of the carcinogenic potency using two-dimensional (2D) descriptors from different software programs. A total of 805 non-congeneric chemicals were extracted from the Carcinogenic Potency Database (CPDBAS). The resulting models had prediction accuracies for internal (training) and external (test) sets as high as 91-93% and 68-70%, respectively. The sensitivity and specificity of the test set were 69-73 and 63-72% correspondingly. High specificity is critical in models for regulatory use that are aimed at ensuring public safety. Thus, the errors that give rise to false negatives are much more relevant. We discuss how we can increase the number of correctly predicted carcinogens using the correlation between the threshold and the values of the sensitivity and specificity.

Investigations of an O-H...S hydrogen bond via Car-Parrinello and path integral molecular dynamics

The presence of intramolecular hydrogen bonds influences the binding energy, tautomeric equilibrium, and spectroscopic properties of various classes of organic molecules. This article discusses the O-H...S bridge, one of the less commonly investigated types of intramolecular interactions. 3-mercapto-1,3-diphenylprop-2-en-1-one was considered as the model structure. This compound exhibits photochromic properties. Car-Parrinello molecular dynamics (CPMD) was applied to investigate the spectroscopic and molecular properties of this compound in the gas phase and in the solid state. The second part of the study is devoted to the effects of the quantization of nuclear motions, with special attention to the O-H...S moiety. Path integral molecular dynamics (PIMD) of the molecular crystal of 3-mercapto-1,3-diphenylprop-2-en-1-one was carried out for this purpose. The employment of this fully quantum mechanical technique enables one to study, in a time-averaged sense, the zero-point motion important for flat potential energy surfaces. Finally, the potentials of mean force (Pmfs) were calculated from the CPMD and PIMD data obtained for the solid-state calculations. The effect of including quantum nuclear motion was investigated. In the studied compound, quantum effects shortened the H-bridge and provided a better description of the free energy minimum. The computational results place this uncommon intramolecular H-bonding among the class of strong hydrogen bonds with large red shifts of O-H stretching modes, which correspond well with previously presented experimental data in the literature concerning this structure.

Spectroscopic properties of a strongly anharmonic Mannich base N-oxide

Car-Parrinello molecular dynamics simulations in vacuum and in the solid state are performed on a strongly anharmonic system, namely, 2-(N-diethylamino-N-oxymethyl)-4,6-dichlorophenol, to investigate its molecular and spectroscopic properties. The investigated compound contains two slightly different molecules in the crystal cell with very short intramolecular hydrogen bonds (of 2.400 and 2.423 A), as determined previously by neutron diffraction. The vibrational properties of the compound are studied on the basis of standard approaches, that is, Fourier transformation of the autocorrelation functions of the atomic velocities and dipole moments. Then, the trajectory obtained from ab initio molecular dynamics is sampled and the obtained snapshots are used to solve the vibrational Schrödinger equations and to calculate the O--H stretching envelope as a superposition of the 0-->1 transition. Using an envelope method, the a posteriori quantum effects are included in the O--H stretching. In addition, NMR spectra are calculated also using the obtained snapshots. One- and two-dimensional potentials of mean force (1D and 2D pmf) are derived to explain the details of the proton dynamics. The computational results are supported by NMR experimental data. In addition, the calculated results are compared with previously published X-ray, neutron diffraction, and spectroscopic descriptions. A detailed analysis of the bridged proton's dynamics is thus obtained. The application of 1D and 2D pmf in a system with a strong bridged-proton delocalization is also demonstrated.

Car-Parrinello simulation of an O-H stretching envelope and potential of mean force of an intramolecular hydrogen bonded system: application to a Mannich base in solid state and in vacuum

Car-Parrinello molecular dynamics (CPMD) study was performed for an anharmonic system-an intramolecularly hydrogen bonded Mannich-base-type compound, 4,5-dimethyl-2(N,N-dimethylaminemethyl)phenol, to investigate the vibrational spectrum associated with the O-H stretching. Calculations were carried out for the solid state and for an isolated molecule. The classical CPMD simulation was performed and then the proton potential snapshots were extracted from the trajectory. The vibrational Schrodinger equation for the snapshots was solved numerically, and the (O-H) envelope was calculated as a superposition of the 0-->1 transitions. The potential of mean force for the proton stretching mode was calculated from the proton vibrational eigenfunctions and eigenvalues incorporating statistical sampling, nuclear quantum effects, and effects of the environment. Perspectives for application of the presented methodology in the computational support of biocatalysis are given in the study.

On the oligomeric state of DJ-1 protein and its mutants associated with Parkinson Disease. A combined computational and in vitro study

Mutations in the DJ-1 protein are present in patients suffering from familial Parkinson disease. Here we use computational methods and biological assays to investigate the relationship between DJ-1 missense mutations and the protein oligomeric state. Molecular dynamics calculations suggest that: (i) the structure of DJ-1 wild type (WT) in aqueous solution, in both oxidized and reduced forms, is similar to the crystal structure of the reduced form; (ii) the Parkinson disease-causing M26I variant is structurally similar to the WT, consistent with the experimental evidence showing the protein is a dimer as WT; (iii) R98Q is structurally similar to the WT, consistent with the fact that this is a physiological variant; and (iv) the L166P monomer rapidly evolves toward a conformation significantly different from WT, suggesting a change in its ability to oligomerize. Our combined computational and experimental approach is next used to identify a mutant (R28A) that, in contrast to L166P, destabilizes the dimer subunit-subunit interface without significantly changing secondary structure elements.

Symmetry-adapted perturbation theory analysis of the N...HX hydrogen bonds

The main aim of the study was the detailed investigation of the interaction energy decomposition in dimers and trimers containing N...HX bonds of different types. The study of angular dependence of interaction energy terms partitioned according to the symmetry-adapted perturbation theory (SAPT) was performed for the dimers containing N...HX bonds as mentioned above: ammonia-HX (X = F, Cl, Br) and pyridine-HF complexes. It was found that the electrostatic and induction terms exhibit strong angular dependence, while the exchange contributions are less affected. The dispersion terms are virtually nondirectional. In addition, the three-body SAPT interaction energy analysis for the mixed acid-base NH3...(HF)2 and (NH3)2...HF trimers revealed strong differences between interactions of similar strength but different types (i.e., hydrogen bond and general electrostatic interaction). The importance of the induction terms for the nonadditivity of the interaction energy in strongly polar systems was confirmed.

Car−Parrinello Molecular Dynamics Study of Anharmonic Systems: A Mannich Base in Solution

A Car-Parrinello molecular dynamics study was performed for 4,5-dimethyl-2-(N,N-dimethylaminomethyl)phenol, a Mannich base, to investigate the vibrational properties in solution of its intramolecular hydrogen bond. The dynamic behavior of this hydrogen-bonded system was investigated using an explicit solvent model. Addition of a nonpolar solvent permitted inclusion of delicate environmental effects on the strongly anharmonic system which was studied from first principles. Molecular dynamics and a posteriori quantization of the O-H motion were applied to reproduce the vibrational features of the O-H stretching mode. Consistent application of Car-Parrinello dynamics based on the density functional theory with subsequent solution of the vibrational Schrödinger equation for the O-H stretching motion offers an effective method for strongly anharmonic systems, and this is supported by the comparison of the results with experimental spectra. As a further element of the intramolecular hydrogen bond study, the effects of deuteration were taken into account and a successful application of the O-H stretching mode quantization technique to the liquid phase is demonstrated. This provides a valuable computational methodology for investigations incorporating nuclear quantum effects in the liquid phase and enzyme active centers and can be used to investigate numerous systems that are not readily susceptible to experimental analysis.

Molecular properties investigation of a substituted aromatic mannich base: dynamic and static models

An analysis of the hydrogen bridge of a Mannich base-type compound [3,5,6-trimethyl-2(N,N-dimethylaminomethyl)phenol, TMM] was performed according to the Car-Parrinello molecular dynamics (CPMD) scheme. A classical treatment of nuclei coupled with a first-principle potential energy surface was obtained from molecular dynamics simulation. Dipole moment values were collected during CPMD trajectory acquisition and subsequently used for the data analysis. The vibrational features and the intramolecular hydrogen-bond properties in the gas phase and solid state of the TMM compound were analyzed on the basis of widely used approaches: Fourier transformation of the autocorrelation function of both the atomic velocities and dipole moments. In addition, the time evolution of the structural parameters related to the hydrogen bond was carried out. The optimally localized Wannier functions served to describe the electronic structure of the Mannich base studied. The second part of the TMM compound study was performed in vacuo on the basis of density functional theory and second-order Møller-Plesset perturbation theory. The potential energy functions were used to solve the 1-D vibrational Schroedinger equation for the proton motion. This enabled a prediction of the anharmonic vibrational levels of the intramolecular hydrogen bond. The description of the electron density topology of the TMM molecule was carried out using the atoms in molecules theoretical framework. The computational results were further compared with the infrared spectra in the solid state.

Synthesis, analgesic activity and computational study of new isothiazolopyridines of Mannich base type

A series of new 4-arylpiperazine derivatives of isothiazolopyridine of Mannich base type and their non-4-arylpiperazine analogues (3 and 4) were synthesized and assayed as potential analgesic agents. Pharmacological assay demonstrated that all the compounds prepared, without exception, displayed significant activity in the mouse writhing assay. The analgesic action, expressed as ED50, was found to be 2-10 times more potent than that of acetylsalicylic acid and 1.5-10 times weaker than that of morphine, these being used as standards. The toxicities (LD50) of the investigated derivatives varied and ranged from 250 to 2000 mg/kg. Additionally, the computational investigations were performed in order to find correlation between molecular structure and biological effects (toxicity, analgesic action) of discussed compounds. Useful model was found for toxicity assessment.

Molecular modeling study of leflunomide and its active metabolite analogues

Leflunomide is known as a compound with various sorts of biological activity, which found a practical application in medicine. Search of current literature revealed an active metabolite of Leflunomide together with its eight analogues synthesized as protein tyrosine kinase inhibitors with potential anticancer activity. Accurate description of the molecular structure of these compounds is valuable. The detailed geometrical parameters description was performed using DFT theory. The conformational analysis and intramolecular proton transfer were considered. Using the most stable conformation the detailed electronic structure description was obtained by analysis of electron density and electrostatic potential distribution in the first step. Next, the topological analysis of the electron density by AIM method and electron localization function (ELF) theories supplemented this study. The AIM and ELF theories were applied to study the topology of the molecules, atomic charges distribution, and details of bonding. The theoretical investigations were performed in the gas phase and by using SCRF/PCM solvent reaction field. In this study the molecular modeling results for Leflunomide and the analogues of its active metabolite are presented.

Kohonen Network Study of Aromatic Compounds Based on Electronic and Nonelectronic Structure Descriptors

Atoms in Molecules (AIM) and Electron Localization Function (ELF) methodologies were applied to describe the electronic structure of 88 aromatic compounds. The analyzed database contains molecules substituted by nucleophilic and electrophilic groups which are responsible for electron density distribution in the molecule and further for its reactivity. Radial Distribution Function (RDF), Weighted Holistic Invariant Molecular (WHIM), Three-Dimensional Molecule Representation of Structures based on Electron Diffraction (3D-MoRSE) and Geometry, Topology and Atom-Weights Assembly (GETAWAY) descriptors were taken into account describing the structures of the analyzed molecules. According to generated descriptor space the classification of the molecules has been subsequently performed using unsupervised learning strategy and Kohonen network. The final step of descriptor space testing was supervised learning of Counter-Propagation Artificial Neural Network (CPANN) using n-octanol/water partition coefficient (logP), dipole moment (DM) and molecular refractivity (MR) as target values.

Structure/activity investigations of 5-substituted 3-methylisoxazole[5, 4-d]1, 2, 3-triazin-4-one derivatives

The series of 5-substituted 3-methylisoxazole[5, 4-d]1, 2, 3-triazin-4-one derivatives was obtained by diazotization of 5-amino-3-methylisoxazol-4-carboxylic acid hydrazide. The immunological activity of these compounds was investigated experimentally in several in vitro and in vivo assays in mice and human models. In the next step, quantum-chemical investigations were performed using density functional theory with the B3LYP hybrid exchange-correlation energy functional and 6-31G(d, p) basis set. The Polarizable Continuum (SCRF/PCM) solvent model was also taken into account in order to show solvent influence on electron density and electrostatic potential around the exemplary molecules. Correlations between molecular structure and biological properties were found using a stepwise selection of scales for the multiple linear regression (MLR).

Density Functional Calculation of the 2D Potential Surface and Deuterium Isotope Effect on 13C Chemical Shifts in Picolinic Acid N-Oxide. Comparison with Experiment

2D free energy surfaces V = V(rOH, rO...O) for the intramolecular H-bond in the title compound were calculated by the DFT method and used in the calculation of primary and secondary chemical shifts of the compound dissolved in chloroform and acetonitrile. Solvent effects were accounted for by the SCRF/PCM method. The corresponding two-dimensional chemical shift surfaces with included solvent reaction field were obtained using the Continuous Set of Gauge Transformations approach at the B3LYP/6-311+G(2d,2p) level of theory. The chemical shifts were estimated as quantum averages along the two internal coordinates in the hydrogen bond and along several vibrational levels according to the Boltzmann distribution at room temperature. Fairly good agreement between the experimental and calculated isotope effects was obtained. 1D and 2D NMR spectra of solutions of picolinic acid N-oxide and its deuterated analogue were recorded and assigned.

Counter-propagation artificial neural network as a tool for the independent variable selection: Structure-mutagenicity study on aromatic amines

The counter-propagation artificial neural network (CP ANN) technique was applied for the independent variable selection and for structure-mutagenic potency modeling on a set of 95 aromatic and heteroaromatic amines with biological activity investigated experimentally by an in vitro assay. The molecular structures were represented by 275 independent variables classified as topostructural, topochemical, geometrical and quantum-chemical descriptors. As a result of the neural network modeling, the following descriptors were found to be the most important for structure-activity relationship: 5 chi -path connectivity index of order h = 5, 3chibC-bond cluster connectivity index of order h = 3, J(B)-Balaban's J index based on bond types, SHSNH2-electrotopological state index values for atoms, phia-flexibility index (kappa p1 x kappa p2/nvx), IC0-mean information content or complexity of a graph based on the 0 order neighborhood of vertices in a hydrogen-filled graph and ELUMO. The leave one out (LOO) method was used in order to test and select the models for mutagenicity prediction. The statistical parameters for the 7-descriptors model are R(Model) = 0.96 and Rcv = 0.85, respectively. In the next step, the number of variables was reduced and the 4-descriptors model was found (R(Model) = 0.95 and Rcv = 0.85) and classified as the best one.