Binding of glycine and L-cysteine on Si(111)-7 x 7

The adsorption of glycine and l-cysteine on Si(111)-7 x 7 was investigated using high-resolution electron energy loss spectroscopy (HREELS) and X-ray photoelectron spectroscopy (XPS). The observation of the characteristic vibrational modes and electronic structures of NH3+ and COO- groups for physisorbed glycine (l-cysteine) demonstrates the formation of zwitterionic species in multilayers. For chemisorbed molecules, the appearance of nu(Si-H), nu(Si-O), and nu(C=Omicron) and the absence of nu(O-H) clearly indicate that glycine and l-cysteine dissociate to produce monodentate carboxylate adducts on Si(111)-7 x 7. XPS results further verified the coexistence of two chemisorption states for each amino acid, corresponding to a Si-NH-CH2-COO-Si [Si-NHCH(CH2SH)COO-Si] species with new sigma-linkages of Si-N and Si-O, and a NH2-CH2-COO-Si [NH2CH(CH2SH)COO-Si] product through the cleavage of the O-H bond, respectively. Glycine/Si(111)-7 x 7 and l-cysteine/Si(111)-7 x 7 can be viewed as model systems for further modification of Si surfaces with biological molecules.     

Bonding and structure of glycine on ordered Al2O3 film surfaces

The interaction between glycine (NH2CH2COOH) layers and an ultrathin Al2O3 film grown epitaxially onto NiAl(110) was studied by temperature-programmed desorption, X-ray photoelectron spectroscopy, ultraviolet photoelectron spectroscopy, work function measurements, and near-edge X-ray absorption fine structure (NEXAFS) spectroscopy. At monolayer coverages at 110 K, there are two coexisting molecular forms: the anionic (NH2CH2COO-) and the zwitterionic form (NH3+CH2COO-) of glycine. As deduced from the photoemission data, the buildup of multilayers at 110 K leads to a condensed phase predominantly in the zwitterionic state. In contrast to the monolayer at 110 K, the monolayer formed at 300 K consists primarily of glycine molecules in the anionic state. The latter species is adsorbed with the oxygen atoms of the carboxylic group pointing toward the substrate. The polarization-dependent C K- and O K-edge NEXAFS spectra indicate that the glycinate species in the monolayer at 300 K is oriented nearly perpendicular to the surface, with the amino group pointing away from the surface.     

Formation of neutral methylcarbamic acid (CH3NHCOOH) and methylammonium methylcarbamate [CH3NH3+][CH3NHCO2-] at low temperature

We study low temperature reactivity of methylamine (CH3NH2) and carbon dioxide (CO2) mixed within different ratios, using FTIR spectroscopy and mass spectrometry. We report experimental evidence that the methylammonium methylcarbamate [CH3NH3(+)][C3NHCO2(-)] and methylcarbamic acid (CH3NHCOOH) are formed when the initial mixture CH3NH2:CO2 is warmed up to temperatures above 40 K. An excess of CH3NH2 favors the carbamate formation while an excess of CO2 leads to a mixture of both methylammonium methylcarbamate and methylcarbamic acid. Quantum calculations show that methylcarbamic acid molecules are associated into centrosymmetric dimers. Above 230 K, the carbamate breaks down into CH3NH2 and CH3NHCOOH, then this latter dissociates into CH3NH2 and CO2. After 260 K, it remains on the substrate a solid residue made of a well-organized structure coming from the association between the remaining methylcarbamic acid dimers. This study shows that amines can react at low temperature in interstellar ices rich in carbon dioxide which are a privileged place of complex molecules formation, before being later released into "hot core" regions.     

Ultrafast dynamics of the carbonyl stretching vibration in acetic acid in aqueous solution studied by sub-picosecond infrared spectroscopy

Vibrational energy relaxation of the carbonyl CO stretching modes of CH3COOD and CD3COOD in D2O is studied by frequency-resolved infrared pump-probe spectroscopy. The spectral change caused by the vibrational excitation includes two dynamical components with the time constants of 450 and 980 fs for CH3COOD and 390 and 930 fs for CD3COOD. The two dynamical components exhibit different spectral properties. There are two species of acetic acid forming different complexes with solvent water molecules. The time constants are almost the same for CH3COOD and CD3COOD, suggesting that the vibrational energy deposited to the carbonyl group is first distributed among vibrational modes not related to the methyl group.     

The formation of the stable radicals .CH2CN, CH3.CHCN and .CH2CH2CN from the anions -CH2CN, CH3-CHCN and -CH2CH2CN in the gas phase. A joint experimental and theoretical study

Franck-Condon one-electron oxidation of the stable anions -CH2CN, CH3-CHCN and -CH2CH2CN (in the collision cell of a reverse-sector mass spectrometer) produce the radicals .CH2CN, CH3.CHCN and .CH2CH2CN, which neither rearrange nor decompose during the microsecond duration of the neutralisation-reionisation experiment. Acetonitrile (CH3CN) and propionitrile (CH3CH2CN) are known interstellar molecules and radical abstraction of these could produce energised .CH2CN and CH3.CHCN, which might react with NH2. (a known interstellar radical) on interstellar dust or ice surfaces to form NH2CH2CN and NH2CH(CH3)CN, precursors of the amino acids glycine and alanine.     

Sequential addition of H2O, CH3OH, and NH3 to Al3O3-: a theoretical study

Photoelectron spectra of two species, Al3O3(H2O)2- and Al3O3(CH3OH)2-, that are produced by the addition of two water or methanol molecules to Al3O3- are interpreted with density-functional geometry optimizations and electron propagator calculations of vertical electron detachment energies. In both cases, there is only one isomer that is responsible for the observed spectral features. A high barrier to the addition of a second molecule may impede the formation of Al3O3N2H6- clusters in an analogous experiment with NH3.     

Understanding the rate of spin-forbidden thermolysis of HN3 and CH3N3

The pyrolysis of the simplest azides HN(3) and CH(3)N(3) has been studied computationally. Nitrogen extrusion leads to the production of NH or CH(3)N. The azides have singlet ground states but the nitrenes CH(3)N and NH have triplet ground states. The competition between spin-allowed decomposition to the excited state singlet nitrenes and the spin-forbidden N(2) loss is explored using accurate electronic structure methods (CASSCF/cc-pVTZ and MR-AQCC/cc-pVTZ) as well as statistical rate theories. Nonadiabatic rate theories are used for the dissociation leading to the triplet nitrenes. For HN(3), (3)NH formation is predicted to dominate at low energy, and the calculated rate constant agrees very well with energy-resolved experimental measurements. Under thermal conditions, however, the singlet and triplet pathways are predicted to occur competitively, with the spin-allowed product increasingly favored at higher temperatures. For CH(3)N(3) thermolysis, spin-allowed dissociation to form (1)CH(3)N should largely dominate at all temperatures, with spin-forbidden formation of (3)CH(3)N almost negligible. Singlet methyl nitrene is very unstable and should rearrange to CH(2)NH immediately upon formation, and the latter species may lose H(2) competitively with vibrational cooling, depending on temperature and pressure.     

Comparison of electron density properties in frozen and relaxed electronic distributions

Two kinds of electron densities for several small molecules (H(2), FH, CH(3)CH(3), CH(3)NH(2), CH(3)OH, and CH(3)F) have been generated for a wide range of bond distances. The first one, as the sum of the electron density of the isolated fragments, and the second one by optimizing the electron density at each given geometrical disposition. A number of properties of this two electronic distributions have been compared (position of the bond critical points, electron density, Laplacian, curvatures, and local energies). The differences, associated to the bond formation, are found to be very important for most of the cases.     

Ultrahigh vacuum deposition of L-cysteine on Au(110) studied by high-resolution X-ray photoemission: from early stages of adsorption to molecular organization

We report on a high-resolution X-ray photoemission spectroscopy study on molecular-thick layers of L-cysteine deposited under ultrahigh vacuum conditions on Au(110). The analysis of core level shifts allowed us to distinguish unambiguously the states of the first-layer molecules from those of molecules belonging to the second layer. The first-layer molecules strongly interact with the metal through their sulfur headgroup. The multipeaked structure of the N 1s, O 1s, and C 1s core levels is interpreted in terms of different molecular moieties. The neutral acidic fraction (HSCH2CH(NH2)COOH) is abundant at low coverage likely associated with isolated molecules or dimers. The zwitterionic phase (HSCH2CH(NH3+)COO-) is largely dominant as the coverage approaches the monolayer limit and is related to the formation of ordered self-assembled molecular structures indicated by electron diffraction patterns. The occurrence of a small amount of cationic molecules (HSCH2CH(NH3+)COOH) is also discussed. The second-layer molecules mainly display zwitterionic character and are weakly adsorbed. Mild annealing up to 100 degrees C leads to the desorption of the second-layer molecules leaving electronic states of the first layer unaltered.     

Changing Rules of Bonding Electron Pair Correlation Energies of CH3X （X = F, OH, NH2） Systems

1 INTRODUCTION It has been known that the electron correlation energy of molecular systems was, and still is, one of the most serious bottleneck problems to the chemis- try accuracy of computational quantum chemistry. Since L鰓din[1] gave the definition …     

A computational study on the structures of methylamine-carbon dioxide-water clusters: evidence for the barrier free formation of the methylcarbamic acid zwitterion (CH3NH2+COO-) in interstellar water ices

We investigated theoretically the interaction between methylamine (CH(3)NH(2)) and carbon dioxide (CO(2)) in the presence of water (H(2)O) molecules thus simulating the geometries of various methylamine-carbon dioxide complexes (CH(3)NH(2)/CO(2)) relevant to the chemical processing of icy grains in the interstellar medium (ISM). Two approaches were followed. In the amorphous water phase approach, structures of methylamine-carbon dioxide-water [CH(3)NH(2)/CO(2)/(H(2)O)(n)] clusters (n = 0-20) were studied using density functional theory (DFT). In the crystalline water approach, we simulated methylamine and carbon dioxide interactions on a fragment of the crystalline water ice surface in the presence of additional water molecules in the CH(3)NH(2)/CO(2) environment using DFT and effective fragment potentials (EFP). Both the geometry optimization and vibrational frequency analysis results obtained from these two approaches suggested that the surrounding water molecules which form hydrogen bonds with the CH(3)NH(2)/CO(2) complex draw the carbon dioxide closer to the methylamine. This enables, when two or more water molecules are present, an electron transfer from methylamine to carbon dioxide to form the methylcarbamic acid zwitterion, CH(3)NH(2)(+)CO(2)(-), in which the carbon dioxide is bent. Our calculations show that the zwitterion is formed without involving any electronic excitation on the ground state surface; this structure is only stable in the presence of water, i.e. in a methyl amine-carbon dioxide-water ice. Notably, in the vibrational frequency calculations on the methylcarbamic acid zwitterion and two water molecules we find the carbon dioxide asymmetric stretch is drastically red shifted by 435 cm(-1) to 1989 cm(-1) and the carbon dioxide symmetric stretch becomes strongly infrared active. We discuss how the methylcarbamic acid zwitterion CH(3)NH(2)(+)CO(2)(-) might be experimentally and astronomically identified by its asymmetric CO(2) stretching mode using infrared spectroscopy.     

Metal aminocarboxylate coordination polymers with chain and layered structures

The synthesis and structures of metal aminocarboxylates prepared in acidic, neutral, or alkaline media have been explored with the purpose of isolating coordination polymers with linear chain and two-dimensional layered structures. Metal glycinates of the formulae [CoCl2(H2O)2(CO2CH2NH3)] (I), [MnCl2(CO2CH2NH3)2] (II), and [Cd3Cl6(CO2CH2NH3)4] (III) with one-dimensional chain structures have been obtained by the reaction of the metal salts with glycine in an acidic medium under hydro/solvothermal conditions. These chain compounds contain glycine in the zwitterionic form. 4-Aminobutyric acid transforms to a cyclic amide under such reaction conditions, and the amide forms a chain compound of the formula [CdBr2(C4H7NO)2] (IV). Glycine in the zwitterionic form also forms a two-dimensional layered compound of the formula [Mn(H2O)2(CO2CH2NH3)2]Br2 (V). 6-Aminocaproic acid under alkaline conditions forms layered compounds with metals at room temperature, the metal being coordinated both by the amino nitrogen and the carboxyl oxygen atoms. Of the two layered compounds [Cd{CO2(CH2)5NH2}2]2 H2O (VI) and [Cu{CO2(CH2)5NH2}2]2 H2O (VII), the latter has voids in which water molecules reside.     

Photoinduced radical processes on the spinel (MgAl2O4) surface involving methane, ammonia, and methane/ammonia

The present study explored photoinduced radical processes caused by interaction of CH(4) and NH(3) with a photoexcited surface of a complex metal oxide: magnesium-aluminum spinel (MgAl(2)O(4); MAS). UV irradiation of MAS in vacuo yielded V-type color centers as evidenced by the 360 nm band in difference diffuse reflectance spectra. Interaction of these H-bearing molecules with photogenerated surface-active hole states (O(S)(-)?) yielded radical species which on recombination produced more complex molecules (including heteroatomic species) relative to the initial molecules. For the MAS/CH(4) system, photoinduced dissociative adsorption of CH(4) on surface-active hole centers produced ?CH(3) radicals that recombined to yield CH(3)CH(3). For MAS/NH(3), a similar dissociative adsorption process led to formation of ?NH(2) radicals with formation of NH(2)NH(2) as an intermediate product; continued UV irradiation ultimately yielded N(2). For the mixed MAS/CH(4)/NH(3) system, however, interaction of adsorbed NH(3) and CH(4) on the UV-activated surface of MAS yielded ?NH(2) and ?CH(3) radicals, respectively, which produced CH(3)-NH(2) followed by loss of the remaining hydrogens to form a surface-adsorbed cyanide, CN(S), species. Recombination of photochemically produced radicals released sufficient energy to re-excite the solid spinel, generating new surface-active sites and a flash luminescence (emission decay time at 520 nm, τ ~ 6 s for the MAS/NH(3) case) referred to as the PhICL effect.     

卤代硅烷(R3SiX)与NR’3形成五配位硅化合物的加成反应

对R3SiX(R=H、CH3; X=F、Cl、Br、I)与NR’3 (R’=H、CH3)的加成物用量子化学密度泛函方法在B3LYP/6-31g(d,p)基组下(X原子采用cep-121g基组)进行了两种加成方式的研究. 一种是NR’3沿Si—X键轴向位置的加成, 另一种是NR’3沿Si—X键侧向接近的加成. 计算结果表明, 前者更稳定且更容易形成加成物; Si上斥电子基团不利于Si—N键的形成, 而N上斥电子基团则有利于Si—N键的形成; NH3-H3SiX系列和N(CH3)3-H3SiX系列均能以两种方式进行加成, NH3-H2(CH3)SiX系列仅能沿Si—X键轴向进行加成, 而NH3-H(CH3)2SiX和NH3-(CH3)3SiX 系列两种方式都不能进行加成; 在同系列加成产物中, 以X=Cl时所得加成物最稳定. 讨论了所有加成物中各键的性能、NBO电荷变化、取代基对加成物结构和稳定性的影响, 并对H3SiX(X=F、Cl、Br、I)与NH3及N(CH3)3加成物在有机溶剂中导电的可能性进行了讨论.     

H3N(CH2)7NH3]8(CH3NH3)2Sn(IV)Sn(II)12I46- a mixed-valent hybrid compound with a uniquely templated defect-perovskite structure

The incorporation of H(3)N(CH(2))(7)NH(3) with CH(3)NH(3)SnI(3) resulted in the formation of a mixed-valent and semiconducting (Eg = 0.84 eV) organic-based perovskite, [H(3)N(CH(2))(7)NH(3)](8)(CH(3)NH(3))(2)Sn(iv)Sn(ii)(12)I(46), with a unique 3D defect-perovskite structure with ordered vacancies at the Sn and I sites.     

烷烃和胺类分子对电子激发态CH(A~2Δ和B~2Σ~-)自由基猝灭

用266nm激光光解CHBr_3分子产生CH(A,B)态自由基,通过测量CH(A,B→X)自发辐射的时间分辨信号测定室温下(CH_3)_2NH、(C_2H_5)_2NH、(C_2H_5)_3N、n-C_5H_(12)、n-C_6H_(14)和n-C_7H_(16)对CH(A,B,v'=0)的猝灭速率常数.发现猝灭速率常数与猝灭剂烷烃分子中的C-H键数近似成线性关系,但对大的烷烃分子,这种增加逐渐趋缓.用碰撞络合物模型计算胺类分子及烷烃分子与CH形成碰撞络合物时的生成截面,结果表明,在电子激发态CH自由基的猝灭过程中,碰撞对子间的多极相互吸引势和色散力作用势可能起重要作用.     

High-pressure- and low-temperature-induced changes in [(CH3)2NH(CH2)2NH3][SbCl5

The structure of N,N-dimethylethylenediammonium pentachloroantimonate(III), [(CH3)2NH(CH2)2NH3][SbCl5], NNDP, was investigated at 100 and 15 K at ambient pressure, as well as at pressures up to 4.00 GPa at room temperature in the diamond-anvil cell. The stable structure at low temperatures and low pressures consists of isolated [SbCl5]2- anions and [(CH3)2NH(CH2)2NH3]2+ cations. The inorganic anions have a distorted square pyramidal geometry. They are arranged in linear chains parallel to the c axis. In contrast to the low-temperature studies, where no phase transition was detected, pressure induces a P2(1)/c --> P2(1)/n phase transition between 0.55 and 1.00 GPa, accompanied by a doubling of the a unit-cell parameter. This solid-solid transition results from changes in the electron configuration of the Sb(III) atom and formation of the Sb-Cl bridging bonds between inorganic polyhedra to form, at approximately 1.0 GPa, isolated [Sb2Cl10]4- units consisting of [SbCl6]3- octahedra and [SbCl5]2- square pyramids connected by a common corner. The intermolecular distances continuously decrease with further increase in pressure, and at approximately 3.1 GPa, zigzag [{SbCl5}n]2n- chains containing corner-sharing [SbCl6]3- octahedra are formed. The unit-cell volume of NNDP decreases by 18.15% between room pressure and 4.00 GPa. The linear distortions of the [SbCl5]2- and [SbCl6]3- polyhedra decrease with increasing pressure and decreasing temperature and indicate a reduction in the stereochemical activity of the lone electron pair on the Sb(III) atom.     

Internal rotation in propionic acid: near-infrared-induced isomerization in solid argon

The conformational system of propionic acid (CH3CH2COOH) is studied in solid argon. It is predicted by the ab initio calculations that this molecule has four stable conformers. These four structures are denoted Tt, Tg+/-, Ct, and Cg+/-, and they differ by the arrangement around the C-O and Calpha-C bonds. The ground-state Tt conformer is the only form present at 8 K after deposition of an argon matrix containing propionic acid. For the CH3CH2COOH and CH3CH2COOD isotopologues, narrow-band excitation of the first hydroxyl stretching overtone of the conformational ground state promotes the Calpha-C and C-O internal rotations producing the Tg+/- and Ct conformers, respectively. A subsequent vibrational excitation of the produced Tg+/- form induces its conversion to the Cg+/- conformer by rotation around the C-O bond. In the dark, all of the produced conformers decay to the conformational ground state at different rates. The decay kinetics and its temperature dependence allow the identification of the conformers by IR absorption spectroscopy, which is supported by ab initio calculations of their vibrational spectra. For the CH3CH2COOD isotopologue, the excitation of molecules isolated in different matrix sites results in site-dependent photoisomerization rates for the Calpha-C and C-O internal rotations, which also confirm the identification of the photoproducts.     

A theoretical investigation of the low energy conformers of the isomers glycine and methylcarbamic acid and their role in the interstellar medium

We have theoretically investigated the low energy conformers of neutral glycine (NH(2)CH(2)COOH) and its isomer methylcarbamic acid (CH(3)NHCOOH) in the gas phase. A total of 16 different levels of the theory, including CCSD(T), MP2 and B3LYP methods with various Pople and Dunning type basis sets with and without polarization and diffuse functions were used. We found eight low energy glycine conformers, where the heavy atoms in three have a planar backbone, and four low energy methylcarbamic acid conformers all with non-planar backbones. Interestingly at all levels of theory, we found that the most stable methylcarbamic acid conformer is significantly lower in energy than the lowest energy glycine conformer. The MP2 level and single point CCSD(T) calculations show the lowest energy methylcarbamic acid conformer to be between 31 to 37 kJ mol(-1) lower in energy than the lowest energy glycine conformer. These calculations suggest that methylcarbamic acid might serve as a precursor to glycine formation in the Interstellar Medium (ISM). We also report the theoretical harmonic vibrational frequencies, infrared intensities, moment of inertia, rotational constants and dipole moments for all of the conformers. In order to understand how glycine or methylcarbamic acid might be formed in the ISM, larger calculations which model glycine or its isomer interacting with several surrounding molecules, such as water, are needed. We demonstrate that B3LYP method should provide a reliable and computationally practical approach to modeling these larger systems.     

Addition of water, methanol, and ammonia to Al3O3- clusters: reaction products, transition states, and electron detachment energies

Products of reactions between the book and kite isomers of Al3O3- and three important molecules are studied with electronic structure calculations. Dissociative adsorption of H2O or CH3OH is highly exothermic and proton-transfer barriers between anion-molecule complexes and the products of these reactions are low. For NH3, the reaction energies are less exothermic and the corresponding barriers are higher. Depending on experimental conditions, Al3O3- (NH3) coordination complexes or products of dissociative adsorption may be prepared. Vertical electron detachment energies of stable anions are predicted with ab initio electron propagator calculations and are in close agreement with experiments on Al3O3- and its products with H2O and CH3OH. Changes in the localization properties of two Al-centered Dyson orbitals account for the differences between the photoelectron spectra of Al3O3- and those of the product anions.