From a localized H3O radical to a delocalized H3O+···e- solvent-separated pair by sequential hydration

The impact of microhydration on the electronic structure and reactivity of the H(3)O moiety is investigated by ab initio calculations. In the gas phase, H(3)O is a radical with spin density localized on its hydrogen end, which is only kinetically stable and readily decomposes into a water molecule and a hydrogen atom. When solvated by a single water molecule, H(3)O preserves to a large extent its radical character, however, two water molecules are already capable to shift most of the spin density to the solvent. With three solvating water molecules this shift is practically completed and the system is best described as a solvent-separated pair of a hydronium cation and a hydrated electron. The electronic structure of this system and its proton transfer reactivity leading to formation of a hydrogen atom already resemble those of a proton-electron pair in bulk water.     

Unimolecular decomposition of chemically activated pentatetraene (H2CCCCCH2) intermediates: A crossed beams study of dicarbon molecule reactions with allene

The reactions dynamics of the dicarbon molecule C2 in the 1Sigma (g)+ singlet ground state and 3Pi(u) first excited triplet state with allene, H2CCCH2(X1A1), was investigated under single collision conditions using the crossed molecular beam approach at four collision energies between 13.6 and 49.4 kJ mol(-1). The experiments were combined with ab initio electronic structure calculations of the relevant stationary points on the singlet and triplet potential energy surfaces. Our investigations imply that the reactions are barrier-less and indirect on both the singlet and the triplet surfaces and proceed through bound C5H4 intermediates via addition of the dicarbon molecule to the carbon-carbon double bond (singlet surface) and to the terminal as well as central carbon atoms of the allene molecule (triplet surface). The initial collision complexes isomerize to form triplet and singlet pentatetraene intermediates (H2CCCCCH2) that decompose via atomic hydrogen loss to yield the 2,4-pentadiynyl-1 radical, HCCCCCH2(X2B1). These channels result in symmetric center-of-mass angular distributions. On the triplet surface, a second channel involves the existence of a nonsymmetric reaction intermediate (HCCCH2CCH) that fragments through atomic hydrogen emission to the 1,4-pentadiynyl-3 radical [C5H3(X2B1)HCCCHCCH]; this pathway was found to account for the backward scattered center-of-mass angular distributions at higher collision energies. The identification of two resonance-stabilized free C5H3 radicals (i.e., 2,4-pentadiynyl-1 and 1,4-pentadiynyl-3) suggests that these molecules can be important transient species in combustion flames and in the chemical evolution of the interstellar medium.     

Surface microscopic structure and electrochemical rectification of a branched alkanethiol self-assembled monolayer

The tert-butanethiol self-assembled monolayers (SAMs) on Au(111) surfaces were prepared from various solvents and investigated by a combination of scanning tunneling microscopy (STM) and electrochemistry in aqueous environments. High-resolution STM images reveal a (radical(7) x radical(7))R19 degrees surface lattice structure, in contrast with the conventional lattice (radical(3) x radical(3))R30 degrees structure for straight-chain alkanethiol SAMs. Interestingly, such a branched monolayer shows electrochemical rectification toward redox probes. We suggest that electrochemical rectification could be a general characteristic of short-chain branched alkanthiol SAMs, and originate in localized electronic effects.     

Isolation of a Neutral Boron‐Containing Radical Stabilized by a Cyclic (Alkyl)(Amino)Carbene

Utilizing a cyclic (alkyl)(amino)carbene (CAAC) as a ligand, neutral CAAC‐stabilized radicals containing a boryl functionality could be prepared by reduction of the corresponding haloborane adducts. The radical species with a duryl substituent was fully characterized by single‐crystal X‐ray structural analysis, EPR spectroscopy, and DFT calculations. Compared to known neutral boryl radicals, the isolated radical species showed larger spin density on the boron atom. Furthermore, the compound that was isolated is extraordinarily stable to high temperatures under inert conditions, both in solution and in the solid state. Electrochemical investigations of the radical suggest the possibility to generate a stable formal boryl anion species.     

Dissociation channels of the 1-buten-2-yl radical and its photolytic precursor 2-bromo-1-butene

The work presented here is the first in a series of studies that use a molecular beam scattering technique to investigate the unimolecular reaction dynamics of C(4)H(7) radical isomers. Photodissociation of the halogenated precursor 2-bromo-1-butene at 193 nm under collisionless conditions produced 1-buten-2-yl radicals with a range of internal energies spanning the predicted barriers to the unimolecular reaction channels of the radical. Resolving the velocities of the stable C(4)H(7) radicals, as well as those of the products, allows for the identification of the energetic onset of each dissociation channel. The data show that radicals with at least 30.7 +/- 2 kcal/mol of internal energy underwent C-C fission to form allene + methyl, and radicals with at least 36.7 +/- 4 kcal/mol of internal energy underwent C-H fission to form H + 1-butyne and H + 1,2-butadiene; both of these observed barriers agree well with the G3//B3LYP calculations of Miller. HBr elimination from the parent molecule was observed, producing vibrationally excited 1-butyne and 1,2-butadiene. In the subsequent dissociation of these C(4)H(6) isomers, the major channel was C-C fission to form propargyl + methyl, and there is also evidence of at least one of the possible H + C(4)H(5) channels. A minor C-Br fission channel produces 1-buten-2-yl radicals in an excited electronic state and with low kinetic energy; these radicals exhibit markedly different dissociation dynamics than do the radicals produced in their ground electronic state.     

Spin densities from subsystem density-functional theory: assessment and application to a photosynthetic reaction center complex model

Subsystem density-functional theory (DFT) is a powerful and efficient alternative to Kohn-Sham DFT for large systems composed of several weakly interacting subunits. Here, we provide a systematic investigation of the spin-density distributions obtained in subsystem DFT calculations for radicals in explicit environments. This includes a small radical in a solvent shell, a π-stacked guanine-thymine radical cation, and a benchmark application to a model for the special pair radical cation, which is a dimer of bacteriochlorophyll pigments, from the photosynthetic reaction center of purple bacteria. We investigate the differences in the spin densities resulting from subsystem DFT and Kohn-Sham DFT calculations. In these comparisons, we focus on the problem of overdelocalization of spin densities due to the self-interaction error in DFT. It is demonstrated that subsystem DFT can reduce this problem, while it still allows to describe spin-polarization effects crossing the boundaries of the subsystems. In practical calculations of spin densities for radicals in a given environment, it may thus be a pragmatic alternative to Kohn-Sham DFT calculations. In our calculation on the special pair radical cation, we show that the coordinating histidine residues reduce the spin-density asymmetry between the two halves of this system, while inclusion of a larger binding pocket model increases this asymmetry. The unidirectional energy transfer in photosynthetic reaction centers is related to the asymmetry introduced by the protein environment.     

Cyclic allene intermediates in intramolecular dehydro Diels-Alder reactions: labeling and theoretical cycloaromatization studies

A comprehensive theoretical and experimental investigation of dehydro Diels-Alder reactions examining the evolution of the cyclic allene intermediates under conditions for intramolecular and ionic and radical intermolecular cycloaromatization processes is reported. Theoretical calculations showed that the most favored intramolecular path for cycloaromatization of 1,2,4-cyclohexatriene 4 and its benzoannulated derivative 14, strained cyclic allenes, consists of a pair of successive [1,2] H shifts rather than a [1,5] shift. Cycloaromatization of cyclic allenes may follow both inter- and intramolecular pathways, depending on the experimental conditions (use of protic or aprotic solvents). For synthetic purposes, the best procedure is to use a protic solvent to promote the ionic intermolecular route, the fastest and highest yielding. When the reaction is carried out in CCl4, intermolecular radical addition of chlorine to the cyclic allene competes with intramolecular aromatization paths. Theoretical calculations predict a low barrier for the reaction of cyclic allenes with carbon tetrachloride, and that the cyclic allenes act as nucleophiles in this reaction.     

Au(111)表面Verdazyl自由基的构象转换

Pure organic radical molecules on metal surfaces are of great significance in exploration of the electron spin behavior. However, only a few of them are investigated in surface studies due to their poor thermal stability. The adsorption and conformational switching of two verdazyl radical molecules, namely, 1, 5-biisopropyl-3-(benzo[b]benzo[4,5]thieno[2, 3-d]thiophen-2-yl)-6-oxoverdazyl (B2P) and 1, 5-biisopropyl-3-(benzo[b]benzo[4,5]thieno[2, 3-d]thiophen-4-yl)-6-oxoverdazyl (B4P), are studied by scanning tunneling microscopy (STM) and density functional theory (DFT). The adsorbed B2P molecules on Au(111) form dimers, trimers and tetramers without any ordered assembly structure in which two distinct appearances of B2P in STM images are observed and assigned to be its "P" and "T" conformations. The "P" conformation molecules appear in the STM image with a large elliptical protrusion and two small ones of equal size, while the "T" ones appear with a large protrusion and two small ones of different size. Likewise, the B4P molecules on Au(111) form dimers at low coverage, strip structure at medium coverage and assembled structure at high coverage which also consists of above-mentioned two conformations. Both B2P molecules and B4P molecules are held together by weak intermolecular interaction rather than chemical bond. STM tip induced conformational switching of both verdayzl radicals is observed at the bias voltage of +2.0 V. The "T" conformation of B2P can be switched to the "P" while the "P" conformation of B4P can be switched to the "T" one. For both molecules, such a conformational switching is irreversible. The DFT calculations with Perdew-Burke-Ernzerhof version exchange-correlation functional are used to optimize the model structure and simulate the STM images. STM images of several possible molecular conformations with different isopropyl orientation and different tilt angle between verdazyl radical and Au(111) surface are simulated. For conformations with different isopropyl orientation, the STM simulated images are similar, while different tilt angles of verdazyl radical lead to significantly different STM simulated images. Combined STM experiments and DFT simulations reveal that the conformational switching originates from the change of tilting angle between the verdazyl radical and Au(111) surface. The tilt angles in "P" and "T" conformations are 0° and 50°, respectively. In this study, two different adsorption conformations of verdazyl radicals on the Au(111) surface are presented and their exact adsorption structures are identified. This study provides a possible way to study the relationship between the electron spin and configuration conversion of pure organic radical molecules and a reference for designing more conformational switchable radical molecules that can be employed as interesting molecular switches.     

Unrestricted Hartree-Fock spin density calculations with orthogonalized atomic orbitals on aza and nitroaromatic radical anions

The spin density distributions in some aza and nitroaromatic radical anions have been calculated using Löwdin's orthogonalized basis set of atomic orbitals in the Unrestricted Hartree-Fock method of Amos and Snyder. The present calculations lead to a satisfactory account of proton splittings in these radicals. Least squares analyses correlating the observed ¹⁴N splittings and the spin density results over completely localized nonorthogonal basis have been separately carried out for aza and nitroaromatic radical anions and the sigma-pi parameters thus obtained are discussed and compared with earlier estimates for these quantities. Unlike the earlier results, the present estimate of Q _NN ^N for aza and nitroaromatic radicals are not very much different from each other.     

Neutral Boryl Radicals in Mixed-Valent B(III)Br-B(II) Adducts

The general strategies to stabilize a boryl radical involve single electron delocalization by π-system and the steric hinderance from bulky groups. Herein, a new class of boryl radicals is reported, with intramolecular mixed-valent B^(III)Br-B^(II) adducts ligated by a cyclic (alkyl)(amino)carbene (CAAC). The radicals feature a large spin density on the boron center, which is ascertained by EPR spectroscopy and DFT calculations. Structural and computational analyses revealed that the stability of radical species was assisted by the CAAC ligand and a weak but significant B(III)Br-B(II) interaction, suggesting a cooperative avenue for stabilization of boryl radicals. Two-electron reduction of these new boryl radicals provides C−H insertion products via a borylene intermediate.     

Photoinduced water splitting with oxotitanium porphyrin: a computational study

The photochemistry of the hydrogen-bonded oxotitanium porphyrin-water complex (TiOP-H(2)O) has been explored with electronic-structure calculations. It is shown that intramolecular charge-transfer processes, which are initiated by the excitation of the Soret band of TiOP, accumulate electronic charge on the oxygen atom of TiOP, which in turn abstracts a hydrogen atom from water by an exoenergetic and essentially barrierless hydrogen-transfer reaction, resulting in the TiPOH˙-OH˙ biradical. About 75% of the absorbed photon energy is thus stored as chemical energy in two ground-state radicals. Absorption of a second photon by TiPOH˙ can result in the detachment of the H˙ radical and recovery of the photocatalyzer TiOP. Again, about 75% of the photon energy is stored in the dissociation energy of TiPOH˙. Overall, a water molecule is decomposed into H˙ and OH˙ radicals by the absorption of two visible photons. Exoenergetic radical recombination reactions can yield molecular hydrogen, molecular oxygen or hydrogen peroxide as closed-shell products.     

STM studies of photochemistry and plasmon chemistry on metal surfaces

We review our recent studies of photochemistry and plasmon chemistry of dimethyl disulfide, (CH₃S)₂, molecules adsorbed on metal surfaces using a scanning tunneling microscope (STM). The STM has been used not only for the observation of surface structures at atomic spatial resolution but also for local spectroscopies. The STM combined with optical excitation by light can be employed to investigate chemical reactions of single molecules induced by photons and localized surface plasmons. This technique allows us to gain insights into reaction mechanisms at a single molecule level. The experimental procedures to examine the chemical reactions using the STM are briefly described. The mechanism for the photodissociation reaction of (CH₃S)₂ molecules adsorbed on metal surfaces is discussed based on both the experimental results obtained with the STM and the electronic structures calculated by density functional theory. The dissociation reaction of the (CH₃S)₂ molecule induced by the optically excited plasmon in the STM junction between a Ag tip and metal substrate is also described. The reaction mechanism and pathway of this plasmon-induced chemical reaction are discussed by comparison with those proposed in plasmon chemistry.     

过硫酸盐和脂肪环胺体系引发机理的ESR研究

用ESR方法研究了过硫酸盐和脂肪环胺吗啉,哌啶及其N-烷基取代衍生物体系引发反应的初级自由基,结合端基分析,证实了这类脂肪环胺与过硫酸盐反应产生的初级自由基都能引发烯类单体聚合。当所用的是脂环仲胺时,其初级自由基为氮中心自由基;用脂环叔胺时,初级自由基是N-烷基的α-碳中心自由基。     

STM studies on porphyrins

Porphyrins are promising components to be used in molecular electronics due to their rich electronic/photonic properties. Preparation of supramolecular architectures of porphyrins on solid surfaces would constitute a basis for further development toward molecular circuitry or other constructs for molecular electronics applications. Assemblies on surfaces can be probed with scanning tunneling microscopy (STM) at submolecular resolutions to reveal the arrangements and conformations of molecules on an individual molecule basis. The electronic characteristics within a single porphyrin molecule can also be probed by means of the same technique. This review summarizes the status quo of STM studies on porphyrins on surfaces with regard to their assemblies, structures, and electronic properties at the single molecule level.     

Modeling deoxyribonucleic acid and ribonucleic acid damage in the gas phase

This short review outlines the tandem mass spectrometric methods for the generation and analysis of transient nucleobase radicals relevant to deoxyribonucleic acid and ribonucleic acid damage. Radical hydrogen atom adducts to uracil, adenine, cytosine and N-methylcytosine were generated by femtosecond electron transfer to the corresponding gas-phase cations in fast beams at 8 keV kinetic energy. Radical unimolecular dissociations were monitored by product analysis following collisional ionization to cations or anions using neutralization-reionization mass spectrometry. The radical energetics and dissociation kinetics were further analyzed by mapping the potential energy surfaces by high-level ab initio calculations in combination with Rice-Remsberger-Kassel-Marcus calculations of unimolecular rate constants. This first- principles-based approach allows one to model radical dissociations occurring from doublet ground electronic states of radical intermediates, assign reaction mechanisms and derive quantitative branching ratios for dissociation channels that are in agreement with experiments. Theoretical analysis also provides distinction between radical dissociations occurring on the ground and excited electronic state potential energy surfaces. Specific characterization of excited state dissociations of nucleobase and other polyatomic radicals remains a challenging topic for both experimentalists and computational chemists.     

Reprint of: Recent advances in the functionalization of allenes via radical process

This review is focused on the recent advances in the functionalization of allenes via radical process. Different radical partners including carbon radicals and heteroatom radicals are discussed in the reactions of allenes. Generally, the radical formed in situ would attack the allene at the central carbon leading to allyl radical intermediate. However, the formation of alkenyl radical intermediate from allene could be observed as well in some cases with high regioselectivity and stereoselectivity.     

Recent advances in the functionalization of allenes via radical process

This review is focused on the recent advances in the functionalization of allenes via radical process. Different radical partners including carbon radicals and heteroatom radicals are discussed in the reactions of allenes. Generally, the radical formed in situ would attack the allene at the central carbon leading to allyl radical intermediate. However, the formation of alkenyl radical intermediate from allene could be observed as well in some cases with high regioselectivity and stereoselectivity.     

Crossed molecular beam study on the reaction of boron atoms, B(2Pj), with allene, H2CCCH2(X1A1)

The reaction of ground state boron atoms, 11B(2Pj), with allene, H2CCCH2(X1A1), was studied under single collision conditions at a collision energy of 21.5 kJ mol(-1) utilizing the crossed molecular beam technique; the experimental data were combined with electronic structure calculations on the 11BC3H4 potential energy surface. The chemical dynamics were found to be indirect and initiated by an addition of the boron atom to the pi-electron density of the allene molecule leading ultimately to a cyclic reaction intermediate. The latter underwent ring-opening to yield an acyclic intermediate H2CCBCH2. As derived from the center-of-mass functions, this structure was long-lived with respect to its rotational period and decomposed via an atomic hydrogen loss through a tight exit transition state to form the closed shell, C2v symmetric H-C is equivalent C-B=CH2 molecule. A brief comparison of the product isomers formed in the reaction of boron atoms with methylacetylene is also presented.     

Simulation of scanning tunneling microscope images of 1,3-cyclohexadiene bound to a silicon surface

Scanning tunneling microscope (STM) images of 1,3-cyclohexadiene bound to silicon are interpreted using a nonequilibrium Green's function method. The resolution of the carbon-carbon double bond for positive bias voltages but not for negative bias voltages is explained using a quasiprobability density analysis. The asymmetry in the images arises from the system's voltage dependent electronic structure. A pi* orbital is found to be responsible for the empty state STM images of the carbon-carbon double bond, which is observed experimentally. The pi orbital relevant for the opposite bias does not produce an STM image sharply localized in the bond region because the molecule induces a Si-surface dipole dependent on the bias. The dipole voltage dependence arises from molecular charging. This result emphasizes the importance of simulating the molecule as an element in an open quantum system.     

A Generalized Unpaired Electron Spin Density Equation and Organic Hyperconjugation Mechanism

A large class of stereochemcial and related interactions in organic chemistry are repulsive and others are attractive, but the relative orientation of two methyl groups and the amount of energy required to twist one relative to the other (the hindered rotation energy barriers), or the alignment of such a group with respect to a conjugated ring to which it is attached (widely attributed to a mechanism called “hyperconjugation”) are estimated to be small in compared with the total energy of the molecule. We used theories of both isotropic and anisotropic proton hyperfine interactions in the π‐electron systems developed in the early sixties. They are approximated by the magnetic dipole nteractions between each proton and an electron spin magnetization that is distributed in 2s and 2p Slater atomic orbitals center on carbon atoms. We have extended these theories to the non‐planar olefinic cation radicals, which are very important in biochemistry as well as in petroleum catalysis. A three dimensional electron spin density equation has been developed in this paper to handle some Jahn‐Teller vibronic molecules. The new electron spin density equation related the observed proton hyperfine splittings to the non‐planar structures of the open‐chain alkene cation radicals generated by radiolysis and various chemical oxidation methods. The spin densities and the conformational calculations based on valence bond theory and symmetry principles are compared with some more elaborated molecular orbital calculations in the literature. The localized valence bond approaches are better in accord with our experimental results. The anomalous line‐width effect of the four methyl groups observed in the 2,3‐dimethyl‐2‐butene cation radicals also confirmed the positive sign of the electron‐proton hyperfine constant of hyper‐conjugation mechanism. A methyl substituent attached to a conjugated molecule often behaves as if it formed part of the region of conjugation; the charge appears to flow from the methyl group into the π electron system and it may also give rise to an appreciable dipole moment. Methylation also gives rise to an appreciable dipole moment, and the resultant red shift of electronic absorption bands is of some importance in the design of dye molecules.