Neutral Molecules Research Articles

Current-Density Calculations on Zn-Porphyrin40 Nanorings.

Two porphyrinoid nanorings have been studied computationally. They were built by linking 40 Zn-porphyrin units with butadiyne bridges. The molecular structures belonging to the D40h point group were fully optimized with the Turbomole program at the density functional theory (DFT) level using the B3LYP functional and the def2-SVP basis sets. The aromatic character was studied at the DFT level by calculating the magnetically induced current-density (MICD) susceptibility using the GIMIC program. The neutral molecules are globally non-aromatic with aromatic Zn-porphyrin units. Charged nanorings could not be studied because almost degenerate frontier orbitals led to vanishing optical gaps for the cations. Since DFT calculations of the MICD are computationally expensive, we also calculated the MICD using three pseudo-π models. Appropriate pseudo-π models were constructed by removing the outer hydrogen atoms and replacing all carbon and nitrogen atoms with hydrogen atoms. The central Zn atom was either replaced with a beryllium atom or with two inner hydrogen atoms. Calculations with the computationally inexpensive pseudo-π models yielded qualitatively the same magnetic response as obtained in the all-electron calculations.

Design and performance of a dual stage asymmetric ion funnel interface

A dual-stage asymmetric ion funnel (DAIF) interface has been designed to remove the bottleneck in ion transmission from atmospheric ionization to the vacuum chamber. This leads to increased sensitivity and improved performance of the mass spectrometer. Both ion funnels are asymmetrically constructed, with a precisely calculated 7 mm radial offset in the ion path. This accelerates the separation of ions from the neutral stream, reduces contamination, and enhances the flow field and vacuum system. The performance of the DAIF interface was investigated through numerical simulations and experimental tests, utilizing the Hexin API-5000 TOFMS as our experimental platform. The results indicate that the asymmetric ion funnel has a powerful desolvation capability, achieving a high transmission efficiency of 87.9%. The novel DAIF interface enhances sensitivity by an order of magnitude. In addition, the robustness of the instrument can be improved by efficiently removing neutral molecules and contaminants from the DAIF. These features make DAIF suitable for various MS systems and ionizations.

Study of The Effect of Solvation on Thermodynamic Parameters

In the present research paper, we study about the effect of solvation on thermodynamic parameters. The main difference between reactions in solution and in the gas, phase is the formation and participation of ions. It is pertinent to consider the process of forming ions. It is pertinent to consider the process of forming ions from neutral molecules and the effect of solvent as the difference between ions in situ and in the gas, phase is the formation and participant of ions.

Synthesis, structure and Hirshfeld surface analysis of a coordination compound of cadmium acetate with 2-amino-benzoxazole.

A first coordination compound of 2-amino-benzoxazole (2AB), namely, bis-(2-amino-benzoxazole-κN 3)bis-(acetato-κ2 O,O')cadmium(II), [Cd(CH3COO)2(2AB)2], has been synthesized from ethanol solutions of Cd(CH3(COO)2 and 2AB. In the monoclinic crystals with the space group C21/c, the cadmium ions coordinate two neutral 2AB mol-ecules in a monodentate fashion through the oxazole N atom, while two acetate ligands are coordinated through the O atoms in a bidentate manner. The coordination polyhedron of the central ion is substanti-ally distorted octa-hedral. There are two relatively strong intra-molecular hydrogen bonds in the complex mol-ecule. Additionally, two inter-molecular hydrogen bonds associate complex mol-ecules into columns running in the [10] and [110] directions. The Hirshfeld surface analysis shows that 45.7% of the inter-molecular inter-actions are from H⋯H contacts, 24.7% are from O⋯H/H⋯O contacts and 18.8% are from C⋯H/H⋯C contacts, while other contributions are from N⋯H/H⋯N and O⋯O contacts.

On the Potential Role of the (Pseudo-) Jahn-Teller Effect in the Membrane Transport Processes: Enniatin B and Beauvericin.

The molecular structure of mycotoxins enniatin B and beauvericin, which are used as ionophores, was studied using density functional theory in various symmetry groups and singly charged states. We have shown that the charge addition or removal causes significant structural changes. Unlike the neutral C3 molecules, the stability of the charged C1 structures was explained by the Jahn-Teller or Pseudo-Jahn-Teller effect. This finding agrees with the available experimental X-ray structures of their metal complexes where electron density transfer from the metal can be expected. Hence, the membrane permeability of metal sandwich-structure complexes possessing antimicrobial activities is modulated by the conformational changes.

Current Design of Mixed-Ligand Complexes of Magnesium(II): Synthesis, Crystal Structure, Thermal Properties and Biological Activity against Mycolicibacterium Smegmatis and Bacillus Kochii

The interaction of Mg2+ with 2-furoic acid (HFur) and oligopyridines, depending on the synthesis conditions, leads to the formation of mixed-ligand complexes [Mg(H2O)4(phen)]·2HFur·phen·H2O (1), [Mg(NO3)2(phen)2] (2) and [Mg3(Fur)6(bpy)2]·3CH3CN (3); these structures were determined with an SC X-ray analysis. According to the X-ray diffraction data, in complex 1, obtained in ambient conditions, the magnesium cation coordinated four water molecules and one phenanthroline fragment, while in complexes 2 and 3 (synthesized in an inert atmosphere), the ligand environment of the complexing agent was represented by neutral oligopyridine molecules and acid anions. The thermal behavior of 1 and 2 was studied using a simultaneous thermal analysis (STA). The in vitro biological activity of complexes 1–3 was studied in relation to the non-pathogenic Mycolicibacterium smegmatis and the virulent strain Mycobacterium tuberculosis H37Rv.

Interaction between drug molecule and inverse spinel surfaces in aqueous solution: Insights from DFT and DMC simulation

In this work, Hartree-Fock (HF), Density function theory (DFT) and dynamical Monte Carlo (DMC) simulations were executed to give information about the adsorption mechanism of clofibric acid (CA) on Mg2TiO4 and Ba2TiO4. Results show that the adsorption efficiency is closely related to global and local quantum chemical parameters. Electronic properties including HOMO-LUMO analysis and NBO charge transfer analysis reveal that the ionic form (CAion) is a more reactive and less stable than the neutral CA molecule. DMC results show that both forms of the drug are adsorbed almost parallel to the surfaces. Mg2TiO4 exhibited high adsorption energy toward the acidic form (−35.056 kcal/mol). From the results, dynamic descriptors show that both forms are adsorbed more strongly on the Mg2TiO4 surface compared to the Ba2TiO4 surface. The short distances between the adsorbates and the adsorbents suggest a chemisorption. Furthermore, the interaction energy values are negative which implies a spontaneous process.

Understanding the boron rejection of cation intercalated multilayered graphene oxide (GO) membrane in reverse osmosis (RO) process: A molecular dynamics study

Cation-intercalated graphene oxide (GO) membrane has emerged as a promising candidate for desalination applications as reverse osmosis (RO) membrane. This study constructs GO membranes with different cations (K+ or Mg2+) and investigates the potential of these membranes in boron removal via nonequilibrium molecular dynamics simulations. In the aquatic environment, boron can exist in the form of boric acid or borate ion, depending on the pH of the solution. As a result, this study considers two forms of boron. This study reveals that the GO membranes effectively reject negatively charged borate ions due to their bigger hydration shell and stronger electrostatic repulsion with the membrane than neutral boric acid molecules. Moreover, K+ ion intercalated GO membranes showed higher boron rejection than Mg2+ ion intercalated GO membranes owing to weaker electrostatic attraction of K+ ions with the boric acid (or borate ions). Additionally, a summary of the effects of oxygen-containing functional groups of the GO membrane on boron rejection is provided. Since the hydroxyl and epoxy functional groups interact with boric acid molecules more strongly, these molecules are prevented from permeating through the membrane. On the other hand, the permeation rate of borate ions declines because of their stronger interactions with the carboxyl functional groups. Furthermore, Mg2+ ion intercalated GO membranes exhibited higher water permeance, excellent Na+ rejection, and poor Cl− rejection compared to K+ ion intercalated GO membranes.

Diffusion Resistance of Segmented Channels.

The geometry of ion and metabolite channels in membranes of biological cells and organelles is usually far from that of a regular right cylinder. Rather, the channels have complex shapes that are characterized by the so-called vestibules and constriction zones which play roles of molecular filters determining the channel selectivity. In the present paper we discuss several channel structures with varying radius that approximate most of the cases found in nature, specifically, channels of smoothly varying radius and channels composed of multiple cylindrical sections of different lengths and radii including channels containing very thin circular constrictions. We consider diffusive transport of electrically neutral molecules driven by the concentration gradient and derive analytical expressions for the diffusion resistance - the integral parameter that describes steady-state transport properties of membrane channels.

Nucleation of Carbonaceous Nanoparticles in a Low Pressure Ar/C2H2 Plasma with C2H4 Impurity.

Computer simulations of one-dimensional multi-fluid equations are used to study the effects of C2H4 addition on the plasma chemistry and formation of nanoparticles in a capacitively coupled Ar/C2H2 plasma. The results indicate that the most important effect is an enhanced production of hydrogen-rich species, especially C4H4. Regarding the effect of C2H4 inlet on different routes of nanoparticles nucleation, it was found that the nucleation via growth of neutral molecules is significantly suppressed, while the radicals and anions remain almost unaffected. As C2H4 participates in many cationic reactions, the concentrations of hydrogen-rich cations are largely enhanced, whereas those of carbon-rich cations are reduced. The numerical results also suggest that the main mechanism behind the production of C6H6 is the insertion of the C2H3 radical into C4H4. The concentrations of the precursors species of C6H6 are increased with an increase in the pressure but are reduced with the applied RF voltage.

Coexistence of Cationic and Anionic Phosphate Moieties in Solids: Unusual but Not Impossible.

Phosphoric acid is commonly known either as a neutral molecule or as an anion (phosphate). We theoretically confirm by ab initio molecular dynamics simulations (AIMD) that a cationic form H4PO4+ coexists with the anionic form H2PO4- in the same salt. This paradoxical situation is achieved by partial substitution of Cs+ by H4PO4+ in CsH2PO4. Thus, HnPO4 acts simultaneously as both the positive and the negative ion of the salt. We analyze the dynamical protonation pattern within the unusual hydrogen bond network that is established between the ions. Our AIMD simulations show that a conventional assignment of protonation states of the phosphate groups is not meaningful. Instead, a better description of the protonation situation is achieved by an efficiently fractional assignment of the strongly hydrogen-bonded protons to both its nearest and next-nearest oxygen neighbors.

Redox‐Responsive Macrocyclic Hosts Based on Calix[4]arene and Calix[4]resorcinarene Scaffolds

AbstractCalix[4]arenes and calix[4]resorcinarenes are well‐known macrocyclic hosts that can be tailored to bind guests of very different natures, including anions, cations, and various neutral molecules. The molecular architectures of the hosts can be altered in many ways: by attaching polar or hydrophilic groups, extending inner cavities with enlarged aromatic side walls, and adding H‐bonding sites to promote the formation of molecular capsules. The attachment of different types of redox‐active moieties renders calix[4]arene and calix[4]resorcinarene derivatives electrochemically active, enabling them to either control the guest‐binding properties of the receptors or be used as electrochemical sensors. This review will focus on calix[4]arene and calix[4]resorcinarene macrocyclic hosts with appended redox‐active groups, such as ferrocene, tetrathiafulvalene, and quinone. We will discuss molecular receptors that can serve as redox sensors for cations or electron‐deficient molecules or can bind and release their guests controlled by redox or electrochemical stimuli.

Exploring the pH-Responsive Interaction of β-Blocker Drug Propranolol with Biomimetic Micellar Media: Fluorescence and Electronic Absorption Studies.

Interaction of neutral and charged lipophilic beta-blocker drug, propranolol (PPL) with biomimicking nanocavities formed by micelles bearing same and opposite charges namely, cationic cetyltrimethylammonium bromide (CTAB), a surface-active ionic liquid 1-hexadecyl-3-methylimidazolium chloride (HDMIC) and anionic sodium dodecyl sulphate (SDS) have been investigated using fluorescence and absorption spectroscopic techniques. Binding of PPL to SDS at pH < pKa is characterised by biphasic interactions with decrease in fluorescence intensity at lower concentrations and subsequent increase post micellization. All the surfactants show significant interactions with the neutral drug molecule at pH > pKa, which is evident from the strongest binding constant ( ) values at pH 10.4. Results of quenching studies indicate that the location of drug molecule is determined by its charge, which is influenced by both pH and charge on micelle surface. For PPL-CTAB and PPL-HDMIC systems, quenching was strongest at pH 10.4, moderate at pH 7.4 and was absent at pH 3.5. However, the PPL-SDS system displayed similar values at all pH conditions, suggesting that the probe is at the same position regardless of pH. Non-covalent interactions, which play crucial role in biological systems, are similarly the primary driving force governing the interaction between PPL and surfactant micelles.

Comparing the Effects of Nuclear and Electron Spins on the Formation of Neutral Hydrogen Molecule

Comparing the Effects of Nuclear and Electron Spins on the Formation of Neutral Hydrogen Molecule

Clusters and bulky Lewis acid protected complexes with planar hexacoordinate beryllium and magnesium.

Planar hexacoordination (ph) is only rarely reported in the literature. So far, only a few neutral and cationic molecules possessing phE (E = C, Si, B, Al, Ga) in the most stable isomer are predicted theoretically. Present electronic structure calculations report hitherto unknown anionic planar hexcoordinate beryllium and magnesium, phBe/Mg, as the most stable isomer. Global minimum searches show that the lowest energy structure of BeC6M3- (M = Al, Ga) and MgC6M3- (M = Ga, In, Tl) is the D3h symmetric phBe/Mg clusters, where beryllium/magnesium is covalently bonded with six carbon centers and M is located in a bridging position between two carbon centers. These global minimum phBe/Mg clusters are highly kinetically stable against isomerization, facilitating the experimental confirmation by photoelectron spectroscopy. Noteworthy is the fact that the phBe/Mg center is linked with carbon centers through three 7c-2e delocalized σ bonds and three 7c-2e π bonds, making the cluster double aromatic (σ + π) in nature. The bonding between the Be/Mg and outer ring moiety can be best expressed as an electron-sharing σ-bond between the s orbital of Be+/Mg+ and C6M32- followed by three dative interactions involving empty pπ and two in-plane p orbitals of Be/Mg. Furthermore, Lewis basic M centers of the title clusters can be passivated through the complexation with bulky Lewis acid, 9-boratriptycene, lowering the overall reactivity of the cluster, which can eventually open up the possibility of their large-scale syntheses.

On the van der Waals interaction between a molecule and a half-infinite plate

We consider a molecule in the Born–Oppenheimer approximation interacting with a plate of infinite thickness, i.e., a half-space, which is perfectly conducting or dielectric. It is well known in the physics literature that in this case the atom or molecule is attracted by the plate at sufficiently large distances. This effect is analogous to the well-known van der Waals interaction between neutral atoms or molecules. We prove that the interaction energy W of the system is given by W(r,v)=−C(v)r−3+O(r−4), where r is the distance between the molecule and the plate and v indicates their relative orientation. Moreover, C(v) is positive and continuous, thus the atom or molecule is always pulled toward the plate at sufficiently large distances, for all relative orientations v. For some specific systems, we provide sharper estimates of W(r, v). This asymptotic behavior is well known in the physics literature; however, we are not aware of any previous rigorous results, even on the existence of a ground state of the system. For pedagogical reasons, we often start with the case of a hydrogen atom and then we generalize the arguments to deal with a general molecule.

Quaternary ammonium ionic liquids based on -SO3H with different alkyl chain lengths as electrolytes for fuel cells and the mechanism for proton transfer in ionic liquid

N, N, N-trimethyl propylsulphonate ammonium hydrosulfate (NC3SO3HHSO4) and N, N, N-trimethyl butyl sulphonate ammonium hydrosulfate (NC4SO3HHSO4) have been synthesized as electrolytes for the fuel cell. The results indicate that the single cell with NC3SO3HHSO4 exhibits a higher maximum power density (MPD) compared to that of the cell with NC4SO3HHSO4. The MPD achieved using NC3SO3HHSO4 and NC4SO3HHSO4 at 50°C were 48.5 mW·cm−2 and 38.2 mW·cm−2, respectively. The diffusion of ions becomes rapid for ionic liquids (ILs) due to their low viscosity, high conductivity, and chemical structure. Furthermore, quantum chemistry calculations provide detailed insights that elucidate the mechanisms underlying the improvement of cell performance. The proton transfer mechanisms in NC3SO3HHSO4 and NC4SO3HHSO4 are further investigated, including the proton transfer between H2SO4 and HSO4−, the proton transfer between cations and their corresponding neutral molecules, as well as the proton transfer between cations and anions. The cell performance improvement mainly depends on proton transfer between cations and their corresponding neutral molecules. The activation energy barriers for the NC3SO3H+-NC3SO3 complex, between the initial structures and the transition state, and between the final structures and the transition state, are 0.67 kcal·mol−1 and 1.55 kcal·mol−1, respectively. However, proton transfer from an NC4SO3H+ to an NC4SO3 does not occur. The difficulty in proton transfer may be attributed to the steric hindrance effect of cations. Therefore, it can be inferred that the steric hindrance effect of cations significantly impacts the mechanism of proton transfer.

Effect of Solvation on Glycine Molecules: A Theoretical Study.

Ab initio calculations of HF+MP2 and DFT-B3LYP quality have been used in calculating the molecular geometries and properties of neutral and charged molecules of glycine in amino acid as well as zwitterionic forms. A traditional set of molecular descriptors has been enriched by the molecular chemical potential, expressed via the Mulliken electronegativity, and Pearson's chemical hardness. In the global energy minimum, the complete vibrational analysis allowed evaluating the standard Gibbs energy and related thermodynamic quantities.

Structural Elucidations of derivatized Sterols using Electrospray Ionization/Atmospheric Pressure Chemical Ionization-Quadrupole Ion Trap-Mass spectrometry

Free sterols are neutral molecules that are difficult to ionize by Electrospray Ionization (ESI) or Atmospheric Pressure Chemical Ionization (APCI). Therefore, in order to increase their ionization efficiency, sterols were converted into their corresponding picolinyl esters. In this study we examined the possibility of analyzing picolinyl ester of sterols derivatives using flow injection ESI-quadrupole ion trap (QIT) MS and APCI-QIT MS and we investigated their fragmentation pathways using low energy collision induced dissociation-tandem mass spectrometry (CID-MS2). This study also aimed to examine the possibility of using ESI-QIT MS3 to identify sterol isomers. The picolinyl esters readily formed protonated molecular ions ([M+H]+) in ESI and APCI sources except for the picolinyl ester of 7-dehydrocholesterol which was detected as the radical cation ion [M].+ using APCI-QIT MS. The ester bonds of picolinyl esters cleaved during CID MS2, resulting in diagnostic fragments corresponding to steryl cation moieties [M+H-C6H5NO2]+. The CID MS3 of [M+H]+ → [M+H-C6H5NO2]+ of picolinyl esters was found to be useful for structural elucidation and for distinguishing among steryl isomers.

Voltage-Mediated Water Dynamics Enables On-Demand Transport of Sugar Molecules in Two-Dimensional Channels.

The constructing of artificial channels with gating functions is an important undertaking for gaining insight into biological process and achieving efficient bionic functions. Typically, controllable transport within such channels relies on either electrostatic or specific interactions between the transporting species and the channel. However, for molecules with weak interactions with the channel, achieving precise gating of the transport remains a significant challenge. In this regard, this study proposes a voltage gating membrane of two-dimensional channels that selectively transport of neutral molecules glucose with a dimension of 0.60 nm. The permeation of glucose is switched on/off by electrochemically manipulating the water dynamics in the nanochannel. Voltage driven-intercalation of ion into the two-dimensional channel causes water to stratify and move closer to the channel walls, thereby resulting in the channel center being emptier for glucose diffusion. Due to the sub-nanometer size dimension of the channel, selective permeation of glucose over sucrose is also achieved in this approach.