Facile Electrochemical Hydrogenation and Chlorination of Glassy Carbon to Produce Highly Reactive and Uniform Surfaces for Stable Anchoring of Thiolated Molecules

Carbon is a highly adaptable family of materials and is one of the most chemically stable materials known, providing a remarkable platform for the development of tunable molecular interfaces. Herein, we report a two‐step process for the electrochemical hydrogenation of glassy carbon followed by either chemical or electrochemical chlorination to provide a highly reactive surface for further functionalization. The carbon surface at each stage of the process is characterized by AFM, SEM, Raman, attenuated total reflectance (ATR) FTIR, X‐ray photoelectron spectroscopy (XPS), and electroanalytical techniques. Electrochemical chlorination of hydrogen‐terminated surfaces is achieved in just 5 min at room temperature with hydrochloric acid, and chemical chlorination is performed with phosphorus pentachloride at 50 °C over a three‐hour period. A more controlled and uniform surface is obtained using the electrochemical approach, as chemical chlorination is observed to damage the glassy carbon surface. A ferrocene‐labeled alkylthiol is used as a model system to demonstrate the genericity and potential application of the highly reactive chlorinated surface formed, and the methodology is optimized. This process is then applied to thiolated DNA, and the functionality of the immobilized DNA probe is demonstrated. XPS reveals the covalent bond formed to be a C?S bond. The thermal stability of the thiolated molecules anchored on the glassy carbon is evaluated, and is found to be far superior to that on gold surfaces. This is the first report on the electrochemical hydrogenation and electrochemical chlorination of a glassy carbon surface, and this facile process can be applied to the highly stable functionalization of carbon surfaces with a plethora of diverse molecules, finding widespread applications.     

Porcelain tile surface modification with isocyanate coupling agent: interactions between EVA modified mortar and silane improving adherence

Adhesion between tiles and mortar is of paramount importance to the overall stability of ceramic tile systems. The interfaces between ceramic tiles and polymer‐modified Portland cement mortar are derived from several physical and chemical phenomena that take place during their formation. From the chemical perspective, weak forces are expected to occur preferably at the tiles and polymer‐modified Portland cement mortar interfaces. Therefore, the purpose of this study was to promote a new chemical functionalization of ceramic tile surfaces by modifying with isocyanate‐trialkoxysilane coupling agent in order to enhance the interfacial adhesion with poly (ethylene‐co‐vinyl acetate), EVA, polymer‐modified mortar. Pull‐off tests and Fourier Transformed Infrared Spectroscopy (FTIR), using the Attenuated Total Reflectance method, were carried out in order to characterize the system. The bond strength results have provided evidence toward improvements in adherence at the tile–polymer modified mortar interface, thus reflecting the development of urethane linkages between silane and EVA polymer, as detected by FTIR. Copyright © 2010 John Wiley & Sons, Ltd.     

The bond bundle in open systems

Much of modern chemistry is concerned with the properties and dynamics of chemical bonds. Although they have been described variously, the most familiar representation is that of a link connecting two atoms. However, no one has yet developed a scheme by which to partition a molecule into bond volumes with well‐defined properties. As a consequence, the chemical bond is left as nothing more than a heuristic devise. Here, we show molecules can be partitioned into bond‐bundles–volumes that share many of the properties associated with the conceptual bond. This partitioning follows naturally through an extension of Baders topological theory of molecular structure. Surprisingly, it also bounds regions of space containing nonbonding or lone‐pair electrons and leads to bond orders consistent with those expected from theories of directed valance. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010     

Palladium in the Chemical Synthesis and Modification of Proteins

The field of site‐specific modification of proteins has drawn significant attention in recent years owing to its importance in various research areas such as the development of novel therapeutics and understanding the biochemical and cellular behaviors of proteins. The presence of a large number of reactive functional groups in the protein of interest and in the cellular environment renders modification at a specific site a highly challenging task. With the development of sophisticated chemical methodologies it is now possible to target a specific site of a protein with a desired modification, however, many challenges remain to be solved. In this context, transition metals in particular palladium‐mediated C−C bond‐forming and C−O bond‐cleavage reactions gained great interest owing to the unique catalytic properties of palladium. Palladium chemistry is being explored for protein modifications in vitro, on the cell surface, and within the cell. Very recently, palladium complexes have been applied for the rapid deprotection of several widely utilized cysteine protecting groups as well as in the removal of solubilizing tags to facilitate chemical protein synthesis. This Minireview highlights these advances and how the accumulated knowledge of palladium chemistry for small molecules is being impressively transferred to synthesis and modification of chemical proteins.     

Proving and Probing the Presence of the Elusive C−H⋅⋅⋅O Hydrogen Bond in Liquid Solutions at Room Temperature

Hydrogen bonds (H bonds) play a major role in defining the structure and properties of many substances, as well as phenomena and processes. Traditional H bonds are ubiquitous in nature, yet the demonstration of weak H bonds that occur between a highly polarized C?H group and an electron‐rich oxygen atom, has proven elusive. Detailed here are linear and nonlinear IR spectroscopy experiments that reveal the presence of H bonds between the chloroform C?H group and an amide carbonyl oxygen atom in solution at room temperature. Evidence is provided for an amide solvation shell featuring two clearly distinguishable chloroform arrangements that undergo chemical exchange with a time scale of about 2 ps. Furthermore, the enthalpy of breaking the hydrogen bond is found to be 6–20 kJ mol^?1. Ab‐initio computations support the findings of two distinct solvation shells formed by three chloroform molecules, where one thermally undergoes hydrogen‐bond making and breaking.     

Development of non‐bonded interaction parameters between graphene and water using particle swarm optimization

New Lennard‐Jones parameters have been developed to describe the interactions between atomistic model of graphene, represented by REBO potential, and five commonly used all‐atom water models, namely SPC, SPC/E, SPC/Fw, SPC/Fd, and TIP3P/Fs by employing particle swarm optimization (PSO) method. These new parameters were optimized to reproduce the macroscopic contact angle of water on a graphene sheet. The calculated line tension was in the order of 10⁻¹¹ J/m for the droplets of all water models. Our molecular dynamics simulations indicate the preferential orientation of water molecules near graphene–water interface with one O H bond pointing toward the graphene surface. Detailed analysis of simulation trajectories reveals the presence of water molecules with ≤∼1, ∼2, and ∼4 hydrogen bonds at the surface of air–water interface, graphene–water interface, and bulk region of the water droplet, respectively. Presence of water molecules with ≤∼1 and ∼2 hydrogen bonds suggest the existence of water clusters of different sizes at these interfaces. The trends observed in the libration, bending, and stretching bands of the vibrational spectra are closely associated with these structural features of water. The inhomogeneity in hydrogen bond network of water at the air–water and graphene–water interface is manifested by broadening of the peaks in the libration band for water present at these interfaces. The stretching band for the molecules in water droplet shows a blue shift as compared to the pure bulk water, which conjecture the presence of weaker hydrogen bond network in a droplet. © 2017 Wiley Periodicals, Inc.     

Charge‐Shift Bonding: A New and Unique Form of Bonding

Charge‐shift bonds (CSBs) constitute a new class of bonds different than covalent/polar‐covalent and ionic bonds. Bonding in CSBs does not arise from either the covalent or the ionic structures of the bond, but rather from the resonance interaction between the structures. This Essay describes the reasons why the CSB family was overlooked by valence‐bond pioneers and then demonstrates that the unique status of CSBs is not theory‐dependent. Thus, valence bond (VB), molecular orbital (MO), and energy decomposition analysis (EDA), as well as a variety of electron density theories all show the distinction of CSBs vis‐à‐vis covalent and ionic bonds. Furthermore, the covalent–ionic resonance energy can be quantified from experiment, and hence has the same essential status as resonance energies of organic molecules, e.g., benzene. The Essay ends by arguing that CSBs are a distinct family of bonding, with a potential to bring about a Renaissance in the mental map of the chemical bond, and to contribute to productive chemical diversity.     

Spatiotemporal Kinetics in Solution Studied by Time‐Resolved X‐Ray Liquidography (Solution Scattering)

Information about temporally varying molecular structure during chemical processes is crucial for understanding the mechanism and function of a chemical reaction. Using ultrashort optical pulses to trigger a reaction in solution and using time‐resolved X‐ray diffraction (scattering) to interrogate the structural changes in the molecules, time‐resolved X‐ray liquidography (TRXL) is a direct tool for probing structural dynamics for chemical reactions in solution. TRXL can provide direct structural information that is difficult to extract from ultrafast optical spectroscopy, such as the time dependence of bond lengths and angles of all molecular species including short‐lived intermediates over a wide range of times, from picoseconds to milliseconds. TRXL elegantly complements ultrafast optical spectroscopy because the diffraction signals are sensitive to all chemical species simultaneously and the diffraction signal from each chemical species can be quantitatively calculated from its three‐dimensional atomic coordinates and compared with experimental TRXL data. Since X‐rays scatter from all the atoms in the solution sample, solutes as well as the solvent, the analysis of TRXL data can provide the temporal behavior of the solvent as well as the structural progression of all the solute molecules in all the reaction pathways, thus providing a global picture of the reactions and accurate branching ratios between multiple reaction pathways. The arrangement of the solvent around the solute molecule can also be extracted. This review summarizes recent developments in TRXL, including technical innovations in synchrotron beamlines and theoretical analysis of TRXL data, as well as several examples from simple molecules to an organometallic complex, nanoparticles, and proteins in solution. Future potential applications of TRXL in femtosecond studies and biologically relevant molecules are also briefly mentioned.     

Late‐Stage Formation of Carbon–Fluorine Bonds

In this account, we review work from our lab on the development of methods for carbon–fluorine bond formation, with an emphasis on late‐stage fluorination of functionalized small molecules and synthesis of ¹⁸F‐labeled molecules for potential use as tracers in positron emission tomography (PET). We attempt to highlight reactions that we feel are of particular practical relevance, as well as areas of research where there is still significant room for advancement.     

A Bioorthogonal Reaction of N‐Oxide and Boron Reagents

The development of bioorthogonal reactions has classically focused on bond‐forming ligation reactions. In this report, we seek to expand the functional repertoire of such transformations by introducing a new bond‐cleaving reaction between N‐oxide and boron reagents. The reaction features a large dynamic range of reactivity, showcasing second‐order rate constants as high as 2.3×10³ M ^?1 s^?1 using diboron reaction partners. Diboron reagents display minimal cell toxicity at millimolar concentrations, penetrate cell membranes, and effectively reduce N‐oxides inside mammalian cells. This new bioorthogonal process based on miniscule components is thus well‐suited for activating molecules within cells under chemical control. Furthermore, we demonstrate that the metabolic diversity of nature enables the use of naturally occurring functional groups that display inherent biocompatibility alongside abiotic components for organism‐specific applications.     

Determination of primary bond scissions by mass spectrometric analysis of ultrasonic degradation products of poly(ethylene oxide‐block‐propylene oxide) copolymers

Ultrasonic degradation of poly(ethylene oxide‐block‐propylene oxide) copolymers consisting of a hydrophilic and a hydrophobic portion was studied with the aim to determine the location of bonds involved in the initial scission of the copolymers. LC–APCI‐IT‐MS and LC–APCI‐orbitrap‐MS were used for the detailed structural analysis of degradation products. The results indicated that initial bond scissions occurred principally at the boundary regions between backbones of polyethylene oxide (PEO) and polypropylene oxide (PPO) chains. Further structural analysis revealed the presence of oxygen adducts in the degradation products. Comparison with a thermal degradation carried out in helium atmosphere, one can conclude that the oxygen adducts are formed by radical reaction with water or dissolving oxygen molecules. The study demonstrated that chemical reactions as well as physical bond stress scissions are involved in the ultrasonic degradation of the copolymers. Copyright © 2010 John Wiley & Sons, Ltd.     

Room‐Temperature Electronic Template Effect of the SmSi(111)‐8×2 Interface for Self‐Alignment of Organic Molecules

This work describes an innovative concept for the development of organized molecular systems based on the template effect of the pre‐structured semi‐conductive SmSi(111) interface. This substrate is selected because Sm deposition in the submonolayer range leads to a 8×2‐reconstruction, which is a well‐defined one‐dimensional semi‐metallic structure. Adsorption of aromatic molecules [1,4‐di‐(9‐ethynyltriptycenyl)‐benzene] on SmSi(111)‐ 8×2 and Si(111)‐7×7 interfaces is investigated by scanning tunneling microscopy (STM) at room temperature. Density functional theory (DFT) and semi‐empirical (ASED+) calculations define the nature of the molecular adsorption sites of the target molecule on SmSi as well as their self‐alignment on this interface. Experimental data and theoretical results are in good agreement.     

Assessment of substituent effects on the parameters of 35Cl nuclear quadrupole resonance in para‐substituted benzene‐sulphenyl chloride via quantum chemical calculations

In this research, substituent effects on the parameters of ³⁵Cl nuclear quadrupole resonance (NQR) in para‐substituted benzene‐sulphenyl chloride were studied at M062X/6‐311G(d,p) theory level. The ³⁵Cl NQR parameters of the quadrupole coupling constant (QCC) and electric‐field gradient (EFG) tensor, as well as an asymmetric parameter, were shown to be correlated with Hammett constant following their calculations. The frontier orbital energy levels, HOMO‐LUMO gaps, hardness, electrophilicity, and chemical potential values of these molecules were calculated as well. natural bond orbital (NBO) analysis was applied for calculating natural populations at chlorine atoms.     

Femtosecond Hydrogen Bond Dynamics of Bulk‐like and Bound Water at Positively and Negatively Charged Lipid Interfaces Revealed by 2D HD‐VSFG Spectroscopy

Interfacial water in the vicinity of lipids plays an important role in many biological processes, such as drug delivery, ion transportation, and lipid fusion. Hence, molecular‐level elucidation of the properties of water at lipid interfaces is of the utmost importance. We report the two‐dimensional heterodyne‐detected vibrational sum frequency generation (2D HD‐VSFG) study of the OH stretch of HOD at charged lipid interfaces, which shows that the hydrogen bond dynamics of interfacial water differ drastically, depending on the lipids. The data indicate that the spectral diffusion of the OH stretch at a positively charged lipid interface is dominated by the ultrafast (<～100 fs) component, followed by the minor sub‐picosecond slow dynamics, while the dynamics at a negatively charged lipid interface exhibit sub‐picosecond dynamics almost exclusively, implying that fast hydrogen bond fluctuation is prohibited. These results reveal that the ultrafast hydrogen bond dynamics at the positively charged lipid–water interface are attributable to the bulk‐like property of interfacial water, whereas the slow dynamics at the negatively charged lipid interface are due to bound water, which is hydrogen‐bonded to the hydrophilic head group.     

键能的分子轨道理论研究 1: 理论公式

从LCAO-MO出发, 给出了一个计算键能的近似方法, 即EAB(i)-∑∑CaiSabCbiεi为第i个占据分子轨道(MO)中的一对电子对A-B键键能的贡献。对所有分子轨道求和即为该键的键能: EAB=∑EAB(i)。按该方法, 不仅可以计算各种不同分子中每两个相键连原子间的键能, 还可以从MO及AO角度分析每一具体键, 如σ, π, δ键的键能以及各AO对键能的贡献。该方法虽有别于求键焓和平衡离解能De, 但计算结果和De的实验值甚相符合。通过对键能的分析研究, 能较好地揭示原子间的相互作用关系及化学键的强弱, 从而可进一步探讨化学反应活性, 反应速率等化学性质。     

The Nature of Chemical Bonds from PNOF5 Calculations

Natural orbital functional theory (NOFT) is used for the first time in the analysis of different types of chemical bonds. Concretely, the Piris natural orbital functional PNOF5 is used. It provides a localization scheme that yields an orbital picture which agrees very well with the empirical valence shell electron pair repulsion theory (VSEPR) and Bent’s rule, as well as with other theoretical pictures provided by valence bond (VB) or linear combination of atomic orbitals–molecular orbital (LCAO‐MO) methods. In this context, PNOF5 provides a novel tool for chemical bond analysis. In this work, PNOF5 is applied to selected molecules that have ionic, polar covalent, covalent, multiple (σ and π), 3c–2e, and 3c–4e bonds.     

Electrochemical TERS Elucidates Potential‐Induced Molecular Reorientation of Adenine/Au(111)

Electrochemical surface activity arises from the interaction and geometric arrangement of molecules at electrified interfaces. We present a novel electrochemical tip‐enhanced Raman spectroscope that can access the vibrational fingerprint of less than 100 small, non‐resonant molecules adsorbed at atomically flat Au electrodes to study their adsorption geometry and chemical reactivity as a function of the applied potential. Combining experimental and simulation data for adenine/Au(111), we conclude that protonated physisorbed adenine adopts a tilted orientation at low potentials, whereas it is vertically adsorbed around the potential of zero charge. Further potential increase induces adenine deprotonation and reorientation to a planar configuration. The extension of EC‐TERS to the study of adsorbate reorientation significantly broadens the applicability of this advanced spectroelectrochemical tool for the nanoscale characterization of a full range of electrochemical interfaces.     

Block copolymer micelles with enzyme molecules at the interfaces

This research provides an efficient method for the fabrication of hybrid micelles with enzyme molecules at the interfaces. Amphiphilic block copolymer is synthesized by reversible addition–fragmentation chain transfer (RAFT) polymerization, and thiol‐modified porcine pancreatic lipase (PPL‐SH) is obtained by treatment of native PPL with Traut's reagent. PPL‐SH is conjugated to the block copolymer chains by thiol‐disulfide exchange reaction. In phosphate buffered saline, the bioconjugate self‐assembles into micelles with enzyme molecules at the interfaces between hydrophobic cores and hydrophilic coronae. The bioactivity of the enzyme molecules on the micelles are compared with the native enzyme. © 2017 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2017 , 55, 2047–2052     

Chemical bonding in view of electron charge density and kinetic energy density descriptors

Stalke's dilemma, stating that different chemical interpretations are obtained when one and the same density is interpreted either by means of natural bond orbital (NBO) and subsequent natural resonance theory (NRT) application or by the quantum theory of atoms in molecules (QTAIM), is reinvestigated. It is shown that within the framework of QTAIM, the question as to whether for a given molecule two atoms are bonded or not is only meaningful in the context of a well‐defined reference geometry. The localized‐orbital‐locator (LOL) is applied to map out patterns in covalent bonding interaction, and produces results that are consistent for a variety of reference geometries. Furthermore, LOL interpretations are in accord with NBO/NRT, and assist in an interpretation in terms of covalent bonding. © 2008 Wiley Periodicals, Inc.J Comput Chem, 2009.