顺、反式结构对MPV异构体的分子构型和吸收光谱的影响

采用量子化学B3LYP／6－31G方法，分别优化；计算了MPV三种异构体的几何和电子结构，结果表明，在异构体中反式结构为平面构型，顺式结构为非平面构型，反式结构增加可使异构体的UV最大吸收峰有规则红移，解释了实验现象，并对烷氧基取代聚对苯乙炔中的顺、反异构其对相关性质的影响进行了有益的讨论。     

Infrared Spectra of Cyanoacetaldehyde (NCCH2CHO): A Potential Prebiotic Compound of Astrochemical Interest

Cyanoacetaldehyde (NC? CH₂CH?O) and its isomer, cyanovinylalcohol (NC? CH?CH? OH), as possible components of the interstellar medium, comets, or planetary atmospheres, exist in equilibrium in the gas phase, although the latter compound is very much in the minority (2 %). The recording and analysis of the gas‐phase infrared spectrum of the former compound within the 4000–500 cm^?1 spectroscopic range and the potential presence of the latter isomer, which could be vital for their detection in these media, are reported. CCSD(T) and G4 high‐level ab initio methods, as well as density functional theory calculations, predict the existence of two stable rotamers of cyanoacetaldehyde. The global minimum has a structure with an unusual O‐C‐C‐C dihedral angle (150°) that falls between the antiperiplanar (180°) and anticlinal forms (120°). The second rotamer, which is about 4.0 kJ mol^?1 less stable in terms of free energy, has a planar structure that corresponds to the synperiplanar form (O‐C‐C‐C dihedral angle: 0°). The absorption vibrational bands of the two aldehyde rotamers that are present in the mixture lead to a spectrum with a very complex structure in the region of deformation movements, in which several low‐intensity bands overlap. A complete and unambiguous assignment of the experimental spectrum has been achieved by using the calculated harmonic and anharmonic vibrational frequencies.     

Spectral Signatures of Hydrogen Thioperoxide (HOSH) and Hydrogen Persulfide (HSSH): Possible Molecular Sulfur Sinks in the Dense ISM

For decades, sulfur has remained underdetected in molecular form within the dense interstellar medium (ISM), and somewhere a molecular sulfur sink exists where it may be hiding. With the discovery of hydrogen peroxide (HOOH) in the ISM in 2011, a natural starting point may be found in sulfur-bearing analogs that are chemically similar to HOOH: hydrogen thioperoxide (HOSH) and hydrogen persulfide (HSSH). The present theoretical study couples the accuracy in the anharmonic fundamental vibrational frequencies from the explicitly correlated coupled cluster theory with the accurate rotational constants provided by canonical high-level coupled cluster theory to produce rovibrational spectra for use in the potential observation of HOSH and HSSH. The ν6 mode for HSSH at 886.1 cm−1 is within 0.2 cm−1 of the gas-phase experiment, and the B0 rotational constant for HSSH of 6979.5 MHz is within 9.0 MHz of the experimental benchmarks, implying that the unknown spectral features (such as the first overtones and combination bands) provided herein are similarly accurate. Notably, a previous experimentally-attributed 2ν1 mode, at 7041.8 cm−1, has been reassigned to the ν1+ν5 combination band based on the present work’s ν1+ν5 value at 7034.3 cm−1. The most intense vibrational transitions for each molecule are the torsions, with HOSH having a more intense transition of 72 km/mol compared to HSSH’s intensity of 14 km/mol. Furthermore, HOSH has a larger net dipole moment of 1.60 D compared to HSSH’s 1.15 D. While HOSH may be the more likely candidate of the two for possible astronomical observation via vibrational spectroscopy due to the notable difference in their intensities, both HSSH and HOSH have large enough net dipole moments to be detectable by rotational spectroscopy to discover the role these molecules may have as possible molecular sulfur sinks in the dense ISM.     

A Journey from Thermally Tunable Synthesis to Spectroscopy of Phenylmethanimine in Gas Phase and Solution

Phenylmethanimine is an aromatic imine with a twofold relevance in chemistry: organic synthesis and astrochemistry. To tackle both aspects, a multidisciplinary strategy has been exploited and a new, easily accessible synthetic approach to generate stable imine-intermediates in the gas phase and in solution has been introduced. The combination of this formation pathway, based on the thermal decomposition of hydrobenzamide, with a state-of-the-art computational characterization of phenylmethanimine laid the foundation for its first laboratory observation by means of rotational electric resonance spectroscopy. Both E and Z isomers have been accurately characterized, thus providing a reliable basis to guide future astronomical observations. A further characterization has been carried out by nuclear magnetic resonance spectroscopy, showing the feasibility of this synthetic approach in solution. The temperature dependence as well as possible mechanisms of the thermolysis process have been examined.     

Self‐Assembly Structures of 1H‐Indazoles in the Solution and Solid Phases: A Vibrational (IR,FIR, Raman,and VCD) Spectroscopy and Computational Study

1H‐indazoles are good candidates for studying the phenomena of molecular association and spontaneous resolution of chiral compounds. Thus, because the 1H‐indazoles can crystallize as dimers, trimers, or catemers, depending on their structure and the phase that they are in, the difficulty in the experimental analysis of the structure of the family of 1H‐indazoles becomes clear. This difficulty leads us to contemplate several questions: How can we determine the presence of different structures of a given molecular species if they change according to the phase? Could these different structures be present in the same phase simultaneously? How can they be determined? To shed light on these questions, we outline a very complete strategy by using various vibrational spectroscopic techniques that are sensitive (VCD) and insensitive (IR, FIR, and Raman) towards the chirality, together with quantum chemical calculations.     

Paramagnetic NMR of Phenolic Oxime Copper Complexes: A Joint Experimental and Density Functional Study

¹H and ¹³C pNMR properties of bis(salicylaldoximato)copper(II) were studied in the solid state using magic‐angle‐spinning NMR spectroscopy and, for the isolated complex and selected oligomers, using density‐functional theory at the PBE0‐ //PBE0‐D3 level. Large paramagnetic shifts are observed, up to δ(¹H)=272 ppm and δ(¹³C)=1006 ppm (at 298 K), which are rationalised through spin delocalisation from the metal onto the organic ligand and the resulting contact shifts arising from hyperfine coupling. The observed shift ranges are best reproduced computationally using exchange‐correlation functionals with a high fraction of exact exchange (such as PBE0‐ ). Through a combination of experimental techniques and first‐principles computation, a near‐complete assignment of the observed signals is possible. Intermolecular effects on the pNMR shifts, modelled computationally in the dimers and trimers through effective decoupling between the local spins via A‐tensor and total spin rescaling in the pNMR expression, are indicated to be small. Addition of electron‐donating substituents and benzannelation of the organic ligand is predicted computationally to induce notable changes in the NMR signal pattern, which suggests that pNMR spectroscopy can be a sensitive probe for the spin distribution in paramagnetic phenolic oxime copper complexes.     

On Ammonia Binding to the Oxygen‐Evolving Complex of Photosystem II: A Quantum Chemical Study

A recent EPR study (M. Perrez Navarro et al., Proc. Natl. Acad. Sci.­ 2013 , 110, 15561) provided evidence that ammonia binding to the oxygen‐evolving complex (OEC) of photosystem II in its S₂ state takes place at a terminal‐water binding position (W1) on the “dangler” manganese center Mn_A. This contradicted earlier interpretations of ¹⁴N electron‐spin‐echo envelope modulation (ESEEM) and extended X‐ray absorption fine‐structure (EXAFS) data, which were taken to indicate replacement of a bridging oxo ligand by an NH₂ unit. Here we have used systematic broken‐symmetry density functional theory calculations on large (ca. 200 atom) model clusters of an extensive variety of substitution patterns and core geometries to examine these contradictory pieces of evidence. Computed relative energies clearly favor the terminal substitution pattern over bridging‐ligand arrangements (by about 20–30 kcal mol^?1) and support W1 as the preferred binding site. Computed ¹⁴N EPR nuclear‐quadrupole coupling tensors confirm previous assumptions that the appreciable asymmetry may be accounted for by strong, asymmetric hydrogen bonding to the bound terminal NH₃ ligand (mainly by Asp61). Indeed, bridging NH₂ substitution would lead to exaggerated asymmetries. Although our computed structures confirm that the reported elongation of an Mn–Mn distance by about 0.15 Å inferred from EXAFS experiments may only be reproduced by bridging NH₂ substitution, it seems possible that the underlying EXAFS data were skewed by problems due to radiation damage. Overall, the present data clearly support the suggested terminal NH₃ coordination at the W1 site. The finding is significant for the proposed mechanistic scenarios of OEC catalysis, as this is not a water substrate site, and effects of this ammonia binding on catalysis thus must be due to more indirect influences on the likely substrate binding site at the O5 bridging‐oxygen position.     

Path Length Determines the Tunneling Decay of Substituted Carbenes

Quantum mechanical tunneling of atoms allows chemical reactions to proceed through barriers too high for thermally activated processes. This causes hydroxycarbenes to decay rapidly and at a temperature‐independent rate even at 11 K. In methylhydroxycarbene, tunneling causes decay through a mechanism that reveals a high but thin barrier rather than an alternative with a lower but broader barrier. No accurate estimates of the widths of such barriers and the lengths of tunneling paths were available. Herein, such a measure is provided by calculating the length of the tunneling paths by using instanton theory. Potential energies are provided by density functional theory verified by explicitly correlated coupled cluster CCSD(T) energies. Our results explain the decay efficiency in the known cases and suggest new substitutions to tune the effects of barrier widths and heights. Fluorination and replacement of the hydroxyl group by a thiol group change the qualitative character of the decay. Methylaminocarbene is predicted to be stable for thousands of years.     

Environmental Effects in Computational Spectroscopy: Accuracy and Interpretation

Spectroscopic techniques are valuable tools for understanding the structure and dynamics of complex systems, such as biomolecules or nanomaterials. Most of the current research is devoted to the development of new experimental techniques for improving the intrinsic resolution of different spectra. However, the subtle interplay of several different effects acting at different length and time scales still makes the interpretation and analysis of such spectra a very difficult task. In this respect, computational spectroscopy is becoming a needful and versatile tool for the assignment and interpretation of experimental spectra. It is in fact possible nowadays to model with relatively high accuracy the physical–chemical properties of complex molecules in different environments, and to link spectroscopic evidence directly to the structural and dynamical properties of optically or magnetically active solvated probes. In this Review, significant steps toward the simulation of entire spectra in condensed phases are presented together with some basic aspects of computational spectroscopy, which highlight how intramolecular and intermolecular degrees of freedom influence several spectroscopic parameters.     

Quantum chemical methods for the investigation of photoinitiated processes in biological systems: theory and applications.

With the advent of modern computers and advances in the development of efficient quantum chemical computer codes, the meaningful computation of large molecular systems at a quantum mechanical level became feasible. Recent experimental effort to understand photoinitiated processes in biological systems, for instance photosynthesis or vision, at a molecular level also triggered theoretical investigations in this field. In this Minireview, standard quantum chemical methods are presented that are applicable and recently used for the calculation of excited states of photoinitiated processes in biological molecular systems. These methods comprise configuration interaction singles, the complete active space self-consistent field method, and time-dependent density functional theory and its variants. Semiempirical approaches are also covered. Their basic theoretical concepts and mathematical equations are briefly outlined, and their properties and limitations are discussed. Recent successful applications of the methods to photoinitiated processes in biological systems are described and theoretical tools for the analysis of excited states are presented.     

Computational study of the vibrational spectra of alpha- and beta-Keggin polyoxometalates

The structures and vibrational frequencies of the alpha- and beta-isomers of the phosphomolybdate Keggin anion [PMo(12)O(40)](3-) have been calculated by using density functional theory. Good agreement between the calculated unscaled vibrational frequencies and those determined experimentally and between the calculated and observed IR traces has been obtained allowing the IR and Raman spectra to be assigned. For the alpha-isomer, the agreement with experiment using the current level of theory is superior to that obtained previously. For the beta-isomer, for which no non-empirical study has previously been reported, the agreement with experiment is slightly poorer but still allows the spectrum to be assigned unambiguously. To calculate the structure and vibrational spectra of these large molydate cluster ions requires large basis sets and a good treatment of electron correlation and relativistic effects. For the 53-atom [PMo(12)O(40)](3-) ions, the computational demands are very high, requiring several months computational time. The calculated IR spectral traces for the two isomers are quite similar due to the relative flexibility of the molybdates, where the slight weakening of the bonding of the rotated trimetallic unit to the rest of the cluster in the beta-isomer is compensated by contraction of the bonds within the unit, and the structure of the [MO(6)] and [PO(4)] units in the two isomers is nearly identical. The vibrations characteristic of the bridging Mo-O-Mo bonds involve both the "2-2" junctions between rotated [M(3)O(13)] units and the "1-2" junctions between rotated and unrotated units. The separation of "ligand" and "interligand" vibrations is not clear. The vibrational analyses confirm the high symmetry, namely T(d) and C(3v) for the alpha- and beta-isomers, respectively, assumed by previous workers in this field. The characteristic group frequencies for the Type I polyoxometalates containing both edge- and corner-sharing I octahedra have been identified.     

Influence of the [2Fe]H Subcluster Environment on the Properties of Key Intermediates in the Catalytic Cycle of [FeFe] Hydrogenases: Hints for the Rational Design of Synthetic Catalysts

Nature's recipe : A theoretical study analyzes how the environment of the [FeFe] hydrogenase's catalytic cofactor affects its chemical properties, particularly the relative stability of complexes with bridging and terminal hydride ligands (see picture; Fe teal, S yellow, C green, N blue, O red, H gray). The results help to elucidate key rules for the design of bioinspired synthetic catalysts for H₂ production.

     

Synthesis, spectroscopic, and electrochemical studies of 1,2-naphthalene-ring-fused tetraazachlorins, -bacteriochlorins, and -isobacteriochlorins: the separation and characterization of structural isomers

1,2-Naphthalene-ring-expanded tetraazachlorins (TACs), tetraazabacteriochlorins (TABCs), and tetraazaisobacteriochlorins (TAiBCs) have been synthesized. Procedures for the synthesis of the starting materials, that is, derivatives of 1,2-naphthalenedicarboxylic acid, have been reinvestigated and improved. Nine possible derivatives, including four, two, and three structural isomers of TACs, TABCs, and TAiBCs, respectively, were separated by using thin-layer chromatography (TLC) or high-performance liquid chromatography (HPLC), and the structure of each isomer was determined by (1)H NMR spectroscopy combined with the NOE technique. The formation ratio of each isomer was rationalized in terms of the intramolecular steric repulsion effect, which was predicted by geometry optimizations at the DFT level. The derived compounds were characterized by using IR, electronic, and magnetic circular dichroism (MCD) spectroscopy, and by electrochemical methods. Frequency calculations at the DFT level correctly reproduced the experimental IR spectra and, in particular, distinguished between the three isomers of the TAiBCs. In the electronic absorption and MCD spectra of the TAC and TABC species, the Q-band splits into two intense components similarly to the 2,3-naphthalene-fused derivatives described in our preceding paper, although no significant spectral differences were observed from species to species. On the other hand, the spectra of the TAiBCs showed moderate differences depending on the structure of the isomer. The spectroscopic properties as well as the electrochemical behavior of these chlorins resemble those of the corresponding benzene-fused derivatives rather than the 2,3-naphthalene-fused derivatives. Molecular-orbital and configuration-interaction calculations within the framework of the ZINDO/S method were helpful in the discussions of the above observations.     

Molecular structure, barriers to internal rotation, and the enthalpy of formation of cumene hydroperoxide PhCMe2OOH: a DFT study

Conformational analysis of cumene hydroperoxide PhCMe₂OOH (1) has been carried out using the density functional methods B3LYP/6-31G(d,p) and B3LYP/6-311+G(3df,2p). Ignoring rotation of methyl groups, molecule 1 has seven conformers differing in orientation of the — CMe₂OOH fragment relative to the benzene ring and in mutual position of atoms in this fragment. The molecular structures, relative energies, and statistical distribution of the conformers were determined, and intramolecular rotational barriers were estimated. The enthalpies of formation of all conformers of molecule 1 were calculated using two approximations with inclusion of zero-point vibrational energy and temperature correction. Calculations using the isodesmic reaction (IDR) scheme made it possible to reduce the systematic error of the determination of the enthalpy of reactions. The total enthalpy of formation of compound 1 calculated with inclusion of statistical distribution of rotamers equals −19.7±3.6 kcal mol⁻¹. The combination of the B3LYP/6-31G(d,p) approximation and the IDR scheme gives fairly accurate results (relative error is ±0.4 kcal mol⁻¹) as compared to those obtained with the extended basis set 6-311+G(3df,2p). Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 6, pp. 1157–1164, June, 2008.