Stark control of a chiral fluoroethylene derivative

Hydrogen dissociation is an unwanted competing pathway if a torsional motion around the C═C double bond in a chiral fluoroethylene derivative, namely (4-methylcyclohexylidene) fluoromethane (4MCF), is to be achieved. We show that the excited state H-dissociation can be drastically diminished on time scales long enough to initiate a torsion around the C═C double bond using the nonresonant dynamic Stark effect. Potential energy curves, dipoles, and polarizabilities for the regarded one-dimensional reaction coordinate are calculated within the CASSCF method. The influence of the excitation and the laser control field is then simulated using wave packet dynamics.     

An ab initio study of the excited States, isomerization energy profiles and conical intersections of a chiral cyclohexylidene derivative

The excited valence and Rydberg states of the chiral (4-methylcyclohexylidene) fluoromethane (4MCF) have been investigated using multiconfigurational CASSCF and CASPT2, and coupled-cluster methods (RI-CC2). A 3s Rydberg state is predicted below the valence (1)pipi* state. To gain insight into the photophysics of the cis-trans isomerization of this olefin, potential energy profiles for the valence (10pipi* state along the twisting and pyramidalization reaction coordinates have been computed using variational methods (CASSCF and multireference configuration interaction with singles and doubles (MR-CISD)). Starting from geometries with energies close to degeneracy in the valence and ground-state curves, three minima on the crossing seam that can be correlated with the conical intersections known for fluoroethylene, have been found. On the basis of these features, the photochemistry of 4MCF is discussed.     

Dynamics of vibrational overtone excitations of H2SO4, H2SO4-H2O: hydrogen-hopping and photodissociation processes

Photochemical processes of sulfuric acid (H2SO4) and sulfuric acid monohydrate (H2SO4-H2O) following overtone excitation of the OH stretching mode are studied by classical trajectory simulations using the semiempirical PM3 potential suface in "on the fly" calculations. The main results are the following: (1) In the excitation of H2SO4 to the fifth OH-stretch overtone, hopping of the H atom between oxygen atoms is found to take place in 22% of the trajectories, only once during simulations of 400 ps. (2) All the trajectories for H2SO4 show a rapid cis-trans isomerization. (3) The photolysis of H2SO4 into SO3 + H2O takes place in 5% of the trajectories on a time scale of approximately 9 ps. (4) Only low overtone levels of H2SO4-H2O have sufficiently long lifetimes to be spectroscopically relevant. Excitation to these OH stretching overtones is found to result in the dissociation of the cluster. H hopping or dissociation of H2SO4 does not take place.     

One transition state leading to two product states: ab initio molecular dynamics simulations of the reaction of formaldehyde radical anion and methyl chloride

Ab initio molecular dynamics (MD) simulations for the reaction of formaldehyde radical anion and methyl chloride indicate that trajectories starting from a well-characterized single transition state reach either an electron-transfer (ET) product or a C-substituted S_N2 product. The two kinds of trajectories have different characteristics. Trajectories which lead to the S_N2 product state are simple, with C–C bond formation and C–Cl bond breaking essentially completed within 50 fs. By contrast, trajectories leading to the ET product are more complex with a sudden electron reorganization taking place around 15–30 fs; the major bonding changes and electron and spin reorganization are completed after 250 fs.     

Photochemical processes induced by vibrational overtone excitations: dynamics simulations for cis-HONO, trans-HONO, HNO3, and HNO3-H2O

Photochemical processes in HNO3, HNO3-H2O, and cis- and trans-HONO following overtone excitation of the OH stretching mode are studied by classical trajectory simulations. Initial conditions for the trajectories are sampled according to the initially prepared vibrational wave function. Semiempirical potential energy surfaces are used in "on-the-fly" simulations. Several tests indicate at least semiquantitative validity of the potential surfaces employed. A number of interesting new processes and intermediate species are found. The main results include the following: (1) In excitation of HNO3 to the fifth and sixth OH-stretch overtone, hopping of the H atom between the oxygen atoms is found to take place in nearly all trajectories, and can persist for many picoseconds. H-atom hopping events have a higher yield and a faster time scale than the photodissociation of HNO3 into OH and NO2. (2) A fraction of the trajectories for HNO3 show isomerization into HOONO, which in a few cases dissociates into HOO and NO. (3) For high overtone excitation of HONO, isomerization into the weakly bound species HOON is seen in all trajectories, in part of the events as an intermediate step on the way to dissociation into OH + NO. This process has not been reported previously. Well-established processes for HONO, including cis-trans isomerization and H hopping are also observed. (4) Only low overtone levels of HNO3-H2O have sufficiently long liftimes to be spectrocopically relevant. Excitation of these OH stretching overtones is found to result in the dissociation of the cluster H hopping, or dissociation of HNO3 does not take place. The results demonstrate the richness of processes induced by overtone excitation of HNO(x) species, with evidence for new phenomena. Possible relevance of the results to atmospheric processes is discussed.     

Conformational preferences and cis-trans isomerization of azaproline residue

The conformational study of N-acetyl-N'-methylamide of azaproline (Ac-azPro-NHMe, the azPro dipeptide) is carried out using ab initio HF and density functional methods with the self-consistent reaction field method to explore the effects of the replacement of the backbone CHalpha group by the nitrogen atom on the conformational preferences and prolyl cis-trans isomerization in the gas phase and in solution (chloroform and water). The incorporation of the Nalpha atom into the prolyl ring results in the different puckering, backbone population, and barriers to prolyl cis-trans isomerization from those of Ac-Pro-NHMe (the Pro dipeptide). In particular, the azPro dipeptide has a dominant backbone conformation D (beta2) with the cis peptide bond preceding the azPro residue in both the gas phase and solution. This may be ascribed to the favorable electrostatic interaction or intramolecular hydrogen bond between the prolyl nitrogen and the amide hydrogen following the azPro residue and to the absence of the unfavorable interactions between electron lone pairs of the acetyl carbonyl oxygen and the prolyl Nalpha. This calculated higher population of the cis peptide bond is consistent with the results from X-ray and NMR experiments. As the solvent polarity increases, the conformations B and B* with the trans peptide bond become more populated and the cis population decreases more, which is opposite to the results for the Pro dipeptide. The conformation B lies between conformations D and A (alpha) and conformation B* is a mirror image of the conformation B on the phi-psi map. The barriers to prolyl cis-trans isomerization for the azPro dipeptide increase with the increase of solvent polarity, and the cis-trans isomerization proceeds through only the clockwise rotation with omega' approximately +120 degrees about the prolyl peptide bond for the azPro dipeptide in the gas phase and in solution, as seen for the Pro dipeptide. The pertinent distance d(N...H-NNHMe) and the pyramidality of imide nitrogen can describe the role of this hydrogen bond in stabilizing the transition state structure and the lower rotational barriers for the azPro dipeptide than those for the Pro dipeptide in the gas phase and in solution.     

Sub-5-fs real-time spectroscopy of transition states in bacteriorhodopsin during retinal isomerization

By using a sub-5-fs visible laser pulse, we have made the first observation of the vibrational spectra of the transition state during trans-cis isomerization in the retinal chromophore of bacteriorhodopsin (bR(S68). No instant isomerization of the retinal occurs in spite of electron promotion from the bonding pi-orbital to the anti-bonding pi*-orbital. The difference between the in-plane and out-of-plane vibrational frequencies (about 1150-1250 and 900-1000 cm(-1), respectively) is reduced during the first time period. The vibrational spectra after this period became very broad and weak and are ascribed to a "silent state." The silent state lasts for 700-900 fs until the chromophore isomerizes to the cis-C13 = C14 conformation. The frequency of the C = C stretching mode was modulated by the torsion mode of the C13 = C14 double bond with a period of 200 fs. The modulation was clearly observed for four to five periods. Using the empirical equation for the relation between bond length and stretching frequency, we determined the transitional C = C bond length with about 0.01 angstroms accuracy during the torsion motion around the double bond with 1-fs time resolution.     

A computational study of ultrafast acid dissociation and acid-base neutralization reactions. II. The relationship between the coordination state of solvent molecules and concerted versus sequential acid dissociation

We investigate the role played by the coordination state of pre-existing water wires during the dissociation of moderately strong acids by means of first-principles molecular dynamics calculations. By preparing 2,4,6-tricyanophenol (calc. pKa～0.5) in two different initial states, we are able to observe sequential as well as concerted trajectories of dissociation: On one hand, equilibrium dissociation takes place on a ～50 ps timescale; proton conduction occurs through three-coordinated water wires in this case, by means of sequential Grotthus hopping. On the other hand, by preparing 2,4,6-tricyanophenol in a hydration state inherited from that of equilibrated phenol (calc. pKa=7.6), the moderately strong acid finds itself in a presolvated state from which dissociation can take place on a ～1 ps timescale. In this case, concerted dissociation trajectories are observed, which consist of proton translocation through two intervening, four-coordinated, water molecules in 0.1-1.0 ps. The present results suggest that, in general, the mechanism of proton translocation depends on how the excess proton is injected into a hydrogen bond network. In particular, if the initial conditions favour proton release to a fourfold H-bonded water molecule, proton translocation by as much as 6-8 A? can take place on a sub-picosecond timescale.     

Dihydrogen to dihydride isomerization mechanism in [(C5Me5)FeH2(Ph2PCH2CH2PPh2)]+ through the experimental and theoretical analysis of kinetic isotope effects

The isomerization of complex [Cp*Fe(dppe)(eta2-H2)]+, generated in situ by low-temperature protonation of Cp*Fe(dppe)H with either HBF4 or CF3COOH, to the dihydride tautomer trans-[Cp*Fe(dppe)(H)2]+ is irreversible and follows first-order kinetics in the -10 to +15 degrees C range with Delta H double dagger = 21.6 +/- 0.8 kcal mol(-1) and DeltaS double dagger = 5 +/- 3 eu. The isomerization rate constant is essentially independent of the nature and quantity of a strong acid. Density functional theory (DFT) calculations on various models, including the complete system at both the quantum mechanics/molecular mechanics (QM/MM) and full QM levels, probe the relative importance of steric and electronic effects for the relative stability of the nonclassical and classical isomers and identify two likely isomerization mechanisms: a "direct" pathway involving simultaneous H-H bond breaking and cis-trans isomerization and a "via Cp" pathway involving agostic C5Me5H intermediates. Both pathways are characterized by activation energies in close correspondence with the experimental value (21.3 and 22.2 kcal mol(-1), respectively). Further kinetic studies were carried out for the Cp*Fe(dppe)H + CF3COOD and Cp*Fe(dppe)D + CF3COOD systems at 273 K. The [Cp*Fe(dppe)(eta2-HD)]+ complex establishes a very rapid isotope redistribution equilibrium with the eta2-H2 and eta2-D2 analogues. The equilibrium constant value (K = 3.3 +/- 0.3) indicates a significant equilibrium isotope effect. Simulation of the rate data provides access to the individual isomerization rate constants kHH, kHD, and kDD for the three isotopomers, yielding kinetic isotope effects: kHH/kHD = 1.24 +/- 0.01 and kHD/kDD = 1.58 +/- 0.01 (and, consequently, kHH/kDD = 1.96 +/- 0.02). The analysis of the DFT-calculated frequencies, using the [Cp*Fe(dhpe)H2]+ model system, for the [Cp*Fe(dhpe)(eta2-XY)]+ isotopomers as well as transition states for the "direct" (TSdir) and "via Cp" (TSrot) pathways (X = H, D) allowed the computation of the expected isotope effects. A comparison with the experiment strongly suggests that the mechanism occurs via the "direct" pathway for the present system, although the small difference in the calculated energy barriers suggests that the "via Cp" pathway may be preferred in other cases.     

Coherent oscillation and ultrafast internal conversion of tetrafluoroethene after excitation at 197 nm.

C2F4 was excited by using a 150 fs pulse in its longest-wavelength band to the Rydberg (3 s) state and then probed by photoionization techniques at 810 nm. The molecule relaxes in two consecutive steps (time constants 29 and 118 fs), probably via the pipi* state, which is lowered in energy by stretching and twisting the C=C bond. A coherent oscillation (350 fs) was found, which we assign to an overtone of the twist vibration (47.6 cm(-1)) in this state. we also conclude that dissociation to singlet and some triplet CF2 only takes place in the hot ground state of C2F4, from where also the C2F4 triplet state is populated. The potentials and their conical intersections are discussed with respect to relaxation and dissociation, including also some new considerations of thermal processes.     

Relative pKa values from first-principles molecular dynamics: the case of histidine deprotonation

Accurate calculation of pK(a) values and free energies for acid/base reactions in the condensed phase has been a long-standing goal of theoretical chemistry. We present a novel application of the Car-Parrinello molecular dynamics method to the problem of relative pK(a) determination. As a particular example, we focus on the second stage in the dissociation of histidine, a process that holds special importance for biology. Using constrained molecular dynamics, we have analyzed the structural, electronic, and dynamical transformations taking place along a preselected, intuitive reaction coordinate. By integrating the potentials of mean force for the deprotonation of histidine and for a reference reaction, autodissociation of water, we obtain a pK(a) value of 6.8, which appears to be in good agreement with the experimental estimate of 6.1. Detailed analysis was undertaken to determine the value of the constraint, which transformed the N*-H* from a covalent to a hydrogen bond. This helped to identify a number of properties that could be successfully used in monitoring the dissociation process. Additional analysis in terms of electron localization functions provided valuable insight into the nature of the deprotonation reaction.     

The role of the beta-ionone ring in the photochemical reaction of rhodopsin

Time-dependent density functional theory (TDDFT) calculations on the photoabsorption process of the 11-cis retinal protonated Schiff base (PSB) chromophore show that the Franck-Condon relaxation of the first excited state of the chromophore involves a torsional twist motion of the beta-ionone ring relative to the conjugated retinyl chain. For the ground state, the beta-ionone ring and the retinyl chain of the free retinal PSB chromophore form a -40 degrees dihedral angle as compared to -94 degrees for the first excited state. The double bonds of the retinal are shorter for the fully optimized structure of the excited state than for the ground state suggesting a higher cis-trans isomerization barrier for the excited state than for the ground state. According to the present TDDFT calculations, the excitation of the retinal PSB chromophore does not primarily lead to a reaction along the cis-trans torsional coordinate at the C11-C12 bond. The activation of the isomerization center seems to occur at a later stage of the photo reaction. The results obtained at the TDDFT level are supported by second-order M?ller-Plesset (MP2) and approximate singles and doubles-coupled cluster (CC2) calculations on retinal chromophore models; the MP2 and CC2 calculations yield for them qualitatively the same ground state and excited-state structures as obtained in the density functional theory and TDDFT calculations.     

Quantum-chemical discussion of cis-trans isomerization of nitrostilbenes during electron transfer and in charge-transfer complexes

Conclusions A new index was proposed, which characterizes the tendency of the nitro derivatives of stilbene to undergo cis-trans isomerization under the conditions of electron transfer or during bonding in a charge-transfer complex. The index represents the integral of overlapping of the idealized antibonding orbital of the exocyclic C=C bond and the molecular orbital of the anion-radical, occupied by one electron. The cis-trans conversion proceeds more easily the greater the degree of localization of the latter on the ethylene bond.Translated from Izvestiya Akademii Nauk SSSR, Seriya Khimicheskaya, No. 5, pp. 1159–1161, May, 1981.We express our gratitude to I. A. Abronin for supplying the program of calculations on the BÉSM-6 electronic computer and to I. V. Stankevich for taking part in discussing the results.     

Isomerization of a peptidic fragment studied theoretically in vacuum and in explicit water solvent at finite temperature

The cis-trans isomerization of N-methylacetamide, a molecular model of the polypeptide chain, is examined via umbrella sampling Car-Parrinello MD and classical MD, in both gas and solution phases at 300 K. A new analysis of the C(O)-N bond interconversion and a full examination of the solvent shell structure are presented.     

Thermal cis–trans isomerization of cis–transoidal polyphenylacetylene

Solution and solid-state thermal cis-trans isomerization of cis–transoidal polyphenylacetylene was investigated. At temperatures higher than 120°C, cis-trans thermal isomerization in solution is accompanied by cyclization, aromatization, and scission of the polymer chain. Both spectral and kinetics data showed that at temperatures lower than 120°C, not only cis-trans thermal isomerization takes place but also intramolecular cyclization.     

第一过渡系金属硅烯配合物的理论研究

以HF/6-311+G^*基组研究了硅烯SiH₂同第一过渡系金属的配合物MSiH₂的分子轨道特征及键解离能.MSiH₂为共平面构型.其中基态的3TiSiH₂和4CoSiH₂带有明显的双键特征.M-Si键具有共价性质.M-Si的键解离能,从Sc到Cu呈现周期性变化,这种变化趋势同M的金属离子激发能之间存在近似的线性关系.     

Stereoelectronic effect on one-electron reductive release of 5-fluorouracil from 5-fluoro-1-(2-oxocycloalkyl)uracils as a new class of radiation-activated antitumor prodrugs

A series of 5-fluoro-1-(2'-oxocycloalkyl)uracils (3-11) that are potentially novel radiation-activated prodrugs for the radiotherapy of hypoxic tumor cells have been synthesized to evaluate a relationship between the molecular structure and the reactivity of one-electron reductive release of antitumor 5-fluorouracil (1) in anoxic aqueous solution. All the compounds 3-11 bearing the 2'-oxo group were one-electron reduced by hydrated electrons (eaq-) and thereby underwent C(1')-N(1) bond dissociation to release 5-fluorouracil 1 in 47-96% yields upon radiolysis of anoxic aqueous solution, while control compounds (12, 13) without the 2'-oxo substituent had no reactivity toward such a reductive C(1')-N(1) bond dissociation. The decomposition of 2-oxo compounds in the radiolytic one-electron reduction was more enhanced, as the one-electron reduction potential measured by cyclic voltammetry in N,N-dimethylformamide became more positive. The efficiency of 5-fluorouracil release was strongly dependent on the structural flexibility of 2-oxo compounds. X-ray crystallographic studies of representative compounds revealed that the C(1')-N(1) bond possesses normal geometry and bond length in the ground state. MO calculations by the AM1 method demonstrated that the LUMO is primarily localized at the pi* orbital of C(5)-C(6) double bond of the 5-fluorouracil moiety, and that the LUMO + 1 is delocalized between the pi* orbital of 2'-oxo substituent and the sigma* orbital of adjacent C(1')-N(1) bond. The one-electron reductive release of 5-fluorouracil 1 in anoxic aqueous solution was presumed to occur from the LUMO + 1 of radical anion intermediates possessing a partial mixing of the antibonding C(2')=O pi* and C(1')-N(1) sigma* MO's, that may be facilitated by a dynamic conformational change to achieve higher degree of (pi* + sigma*) MO mixing.     

A single transition state serves two mechanisms. The branching ratio for CH2O*- + CH3Cl on improved potential energy surfaces

The reaction of formaldehyde radical anion with methyl chloride, CH2O*- + CH3Cl, is an example in which a single transition state leads to two products: substitution at carbon (Sub(C), CH3CH2O* + Cl-) and electron transfer (ET, CH2O + CH3* + Cl-). The branching ratio for this reaction has been studied by ab initio molecular dynamics (AIMD). The energies of transition states and intermediates were computed at a variety of levels of theory and compared to accurate energetics calculated by the G3 and CBS-QB3 methods. A bond additivity correction has been constructed to improve the Hartree-Fock potential energy surface (BAC-UHF). A satisfactory balance between good energetics and affordable AIMD calculations can be achieved with BH&HLYP/6-31G(d) and BAC-UHF/6-31G(d) calculations. Approximately 200 ab initio classical trajectories were calculated for each level of theory with initial conditions sampled from a thermal distribution at 298 K at the transition state. Three types of trajectories were distinguished: trajectories that go directly to ET product, trajectories that go to Sub(C) product, and trajectories that initially go into the Sub(C) valley and then dissociate to ET products. The BH&HLYP/6-31G(d) calculations overestimate the number of nonreactive and direct ET trajectories because the transition state is too early. For the BH&HLYP and BAC-UHF methods, about one-third of the trajectories that initially go into the Sub(C) valley dissociate to ET products, compared to just over half with UHF/6-31G(d) in the earlier study. This difference can be attributed to a better value for the calculated energy release from the initial transition state and to an improved Sub(C) --> ET barrier height with the BH&HLYP and BAC-UHF methods.     

Conjecture: imines as unidirectional photodriven molecular motors-motional and constitutional dynamic devices

Compounds containing the C==N group, such as imines and their derivatives, may undergo syn-anti isomerization by two different routes: 1) photochemically, by out-of-plane rotation around the carbon-nitrogen double bond through a "perpendicular" form, and 2) thermally, by in-plane nitrogen inversion through a "linear" transition state. When the two interconversions occur in sequence, a full, closed process is accomplished, restoring the initial state of the system along two different steps. In a chiral imine-type compound, for example, with an asymmetric center next to the C==N function, photoinduced rotation may be expected to occur in one sense in preference to the opposite one. Thus, photoisomerization followed by thermal isomerization in a chiral imine compound generates unidirectional molecular motion. Generally, imine-type compounds represent unidirectional molecular photomotors converting light energy into mechanical motion. As they are also able to undergo exchange of the carbonyl and amine partners, they present constitutional dynamics. Thus, imine-type compounds are double dynamic, motional, and constitutional devices.     

Isomerization and dissociation dynamics of HCN in a picosecond infrared laser field: a full-dimensional classical study

We report a full-dimensional study of the classical dynamics of HCN-->HNC isomerization and of HCN rovibrational dissociation driven by a strong but nonionizing picosecond infrared laser field. The dynamics of the isolated molecule and of the molecule in liquid Ar have both been studied. Our theoretical and numerical results show that when all degrees of freedom are accounted for the field induced molecular dynamics can be totally different from what was found in previous studies, where the HCN molecule is restricted to a plane containing the external field. It is shown that as HCN is driven by an infrared laser field, the rotation of the H atom around the C-N bond provides an important and highly efficient energy absorption mechanism. In the presence of a monochromatic picosecond infrared laser field with an intensity of 10(13) W/cm(2), this energy absorption mechanism generates considerable HCN-->HNC isomerization yield or high rovibrational dissociation yield without molecular preorientation or prealignment. Our study of the field induced isomerization and dissociation dynamics of the same system in liquid Ar shows that the picosecond isomerization dynamics is insignificantly affected by the surrounding atomic liquid whereas the dissociation yield may be greatly suppressed in a high density liquid. The implications of this study for full-dimensional quantum dynamics of multiphoton rovibrational excitation and dissociation of triatomics are briefly discussed.