Laser probes of conformational isomerization in flexible molecules and complexes

Molecules with several flexible coordinates have potential energy surfaces with a large number of minima and many transition states separating them. A general experimental protocol is described that is capable of studying conformational isomerization in such circumstances, measuring the product quantum yields following conformation-specific infrared excitation, and measuring energy thresholds for isomerization of specific X --> Y reactant-product isomer pairs following excitation via stimulated emission pumping (SEP). These methods have been applied to a series of molecules of varying size and conformational complexity, including 3-indolepropionic acid (IPA), meta-ethynylstyrene, N-acetyltryptophan methyl amide (NATMA), N-acetyltryptophan amide (NATA), and melatonin. Studies of isomerization in solute-solvent complexes are also described, including a measurement of the barrier to isomerization in the IPA-H2O complex, and a unique isomerization reaction in which a single water molecule is shuttled between H-bonding sites on the trans-formanilide (TFA) molecule.     

Infrared-induced conformational isomerization and vibrational relaxation dynamics in melatonin and 5-methoxy-N-acetyl tryptophan methyl amide

The conformational isomerization dynamics of melatonin and 5-methoxy N-acetyltryptophan methyl amide (5-methoxy NATMA) have been studied using the methods of IR-UV hole-filling spectroscopy and IR-induced population transfer spectroscopy. Using these techniques, single conformers of melatonin were excited via a well-defined NH stretch fundamental with an IR pump laser. This excess energy was used to drive conformational isomerization. By carrying out the infrared excitation early in a supersonic expansion, the excited molecules were re-cooled into their zero-point levels, partially re-filling the hole created in the ground state population of the excited conformer, and creating gains in population of the other conformers. These changes in population were detected using laser-induced fluorescence downstream in the expansion via an UV probe laser. The isomerization quantum yields for melatonin show some conformation specificity but no hint of vibrational mode specificity. In 5-methoxy NATMA, no isomerization was observed out of the single conformational well populated in the expansion in the absence of the infrared excitation. In order to study the dependence of the isomerization on the cooling rate, the experimental arrangement was modified so that faster cooling conditions could be studied. In this arrangement, the pump and probe lasers were overlapped in space in the high density region of the expansion, and the time dependence of the zero-point level populations of the conformers was probed following selective excitation of a single conformation. The analysis needed to extract isomerization quantum yields from the timing scans was developed and applied to the melatonin timing scans. Comparison between the frequency and time domain isomerization quantum yields under identical experimental conditions produced similar results. Under fast cooling conditions, the product quantum yields were shifted from their values under standard conditions. The results for melatonin are compared with those for N-acetyl tryptophan methyl amide.     

Theoretical study of isomerization and dissociation transition states of C3H5O radical isomers: ab initio characterization of the critical points and statistical transition-state theory modeling of the dynamics

I use coupled-cluster theory and a modest basis set, aug-cc-pVDZ, to calculate structures and harmonic vibrational frequencies of local minima and transition states on the C(3)H(5)O potential energy surface. Accurate energies are computed using explicitly correlated coupled-cluster methods and a large basis set, cc-pVQZ-F12, to approach the one-particle basis set limit. My computations characterize eight additional stable radical structures on the global potential energy surface for this system. Additionally, this study encompasses many more isomerization and dissociation pathways, both between previously known intermediates and ones first characterized here. Analysis of the transition states and statistical transition-state theory results shows that energetically small barriers connect many of the alkenol and epoxide intermediates to the straight-chain alkoxy isomers, leading to significant branching to these alkoxy radical intermediates. Facile isomerization to these alkoxy intermediates is significant because the barrier heights leading to H + acrolein and HCO + C(2)H(4) product channels are energetically accessible even at low vibrational energies. The low dissociation barrier heights and loose transition states of these pathways result in unimolecular dissociation as opposed to isomerization to a different C(3)H(5)O intermediate.     

The dynamics of conformational isomerization in flexible biomolecules. I. Hole-filling spectroscopy of N-acetyl tryptophan methyl amide and N-acetyl tryptophan amide

The conformational isomerization dynamics of N-acetyl tryptophan methyl amide (NATMA) and N-acetyl tryptophan amide (NATA) have been studied using the methods of IR-UV hole-filling spectroscopy (HFS) and IR-induced population transfer spectroscopy (IR-PTS), which were developed for this purpose. Single conformations of these molecules were selectively excited in well-defined NH stretch fundamentals. This excess energy was used to drive conformational isomerization. By carrying out the infrared excitation early in a supersonic expansion, the excited molecules were recooled into their zero-point levels, partially refilling the hole created in the ground state population of one of the conformers, and creating gains in population in other conformers. These changes in population were detected using laser-induced fluorescence downstream in the expansion. In HFS, the IR wavelength is fixed and the UV laser tuned in order to determine where the population went following selective infrared excitation. In IR-PTS, the UV is fixed to monitor the population of a given conformation, and the IR is tuned to record the IR-induced changes in the population of the monitored conformer. Besides demonstrating the capability of the experiment to change the downstream conformational population distribution, the IR-PTS scans were used to extract two quantitative results: (i) The fractional populations of the conformers in the absence of the infrared, and (ii) the isomerization quantum yields for each of the six unique amide NH stretch fundamentals (three conformers each with two amide groups). The method for obtaining quantum yields is described in detail. In both NATMA and NATA, the quantum yields show modest conformational specificity, but only a hint of vibrational mode specificity. The prospects for the hole-filling technique for providing insight into energy flow in large molecules are discussed, leaving a more detailed theoretical modeling to the adjoining paper [Evans et al. J. Chem. Phys. 120, 148 (2004)].     

Overtone-induced dissociation and isomerization dynamics of the hydroxymethyl radical (CH2OH and CD2OH). I. A theoretical study

The dissociation of the hydroxymethyl radical, CH(2)OH, and its isotopolog, CD(2)OH, following the excitation of high OH stretch overtones is studied by quasi-classical molecular dynamics calculations using a global potential energy surface (PES) fitted to ab initio calculations. The PES includes CH(2)OH and CH(3)O minima, dissociation products, and all relevant barriers. Its analysis shows that the transition states for OH bond fission and isomerization are both very close in energy to the excited vibrational levels reached in recent experiments and involve significant geometry changes relative to the CH(2)OH equilibrium structure. The energies of key stationary points are refined using high-level electronic structure calculations. Vibrational energies and wavefunctions are computed by coupled anharmonic vibrational calculations. They show that high OH-stretch overtones are mixed with other modes. Consequently, trajectory calculations carried out at energies about ~3000 cm(-1) above the barriers reveal that despite initial excitation of the OH stretch, the direct OH bond fission is relatively slow (10 ps) and a considerable fraction of the radicals undergoes isomerization to the methoxy radical. The computed dissociation energies are: D(0)(CH(2)OH → CH(2)O + H) = 10,188 cm(-1), D(0)(CD(2)OH → CD(2)O + H) = 10,167 cm(-1), D(0)(CD(2)OH → CHDO + D) = 10,787 cm(-1). All are in excellent agreement with the experimental results. For CH(2)OH, the barriers for the direct OH bond fission and isomerization are: 14,205 and 13,839 cm(-1), respectively.     

Large-amplitude dynamics in vinyl radical: the role of quantum tunneling as an isomerization mechanism

We report tunneling splittings associated with the large amplitude 1,2 H-atom migration to the global minima in the vinyl radical. These are obtained using a recent full-dimensional ab initio potential energy surface (PES) [A. R. Sharma, B. J. Braams, S. Carter, B. C. Shepler, and J. M. Bowman, J. Chem. Phys. 130(17), 174301 (2009)] and independently, directly calculated "reaction paths." The PES is a multidimensional fit to coupled cluster single and double and perturbative treatment of triple excitations coupled-cluster single double triple (CCSD(T)) with the augmented correlation consistent triple zeta basis set (aug-cc-pVTZ). The reaction path potentials are obtained from a series of CCSD(T)/aug-cc-pVnTZ calculations extrapolated to the complete basis set limit. Approximate 1D calculations of the tunneling splitting for these 1,2-H atom migrations are obtained using each of these potentials as well as quite different 1D Hamiltonians. The splittings are calculated over a large energy ranges, with results from the two sets of calculations in excellent agreement. Though negligibly slow (>1 s) for the vibrational ground state, this work predicts tunneling-promoted 1,2 hydride shift dynamics in vinyl to exhibit exponential growth with internal vibrational excitation, specifically achieving rates on the sub-μs time scale at energies above E ≈ 7500 cm(-1). Most importantly, these results begin to elucidate the possible role of quantum isomerization through barriers without dissociation, in competition with the more conventional picture of classical roaming permitted over a much narrower window of energies immediately below the bond dissociation limit. Furthermore, when integrated over a Boltzmann distribution of thermal energies, these microcanonical tunneling rates are consistent with sub-μs time scales for 1,2 hydride shift dynamics at T > 1400 K. These results have potential relevance for combustion modeling of low-pressure flames, as well as recent observations of nuclear spin statistical mixing from high-resolution IR/microwave spectroscopy on vinyl radical.     

Rotational isomerism of acetic acid isolated in rare-gas matrices: Effect of medium and isotopic substitution on IR-induced isomerization quantum yield and cis-->trans tunneling rate

Rotational isomerization of acetic acid (CH3COOH) is studied in Ar, Kr, and Xe matrices. The light-induced trans-->cis reaction is promoted using resonant excitation of a number of modes in the 3500-7000 cm(-1) region, and the quantum yields for this process are measured for various acetic acid isotopologues and matrix materials. For excitation of acetic acid at energies above the predicted isomerization energy barrier (> or =4400 cm(-1)), the measured quantum yields are in average 2%-3%, and this is one order of magnitude smaller than the corresponding values known for formic acid (HCOOH). This difference is interpreted in terms of the presence of the methyl group in acetic acid, which enhances energy relaxation channels competing with the rotational isomerization. This picture is supported by the observed large effect of deuteration of the methyl group on the photoisomerization quantum yield. The trans-->cis reaction quantum yields are found to be similar for Ar, Kr, and Xe matrices, suggesting similar energy relaxation processes for this molecule in the various matrices. The IR-induced cis-->trans process, studied for acetic acid deuterated in the hydroxyl group, shows reliably larger quantum yields as compared with the trans-->cis process. For pumping of acetic acid at energies below the predicted isomerization barrier, the trans-->cis reaction quantum yields decrease strongly when the photon energy decreases, and tunneling is the most probable mechanism for this process. For the cis-->trans dark reaction, the observed temperature and medium effects indicate the participation of the lattice phonons in the tunneling-induced process.     

Prediction of product branching ratios in the C(3P)+C2H2-->l-C3H+H/c-C3H+H/C3+H2 reaction using ab initio coupled clusters calculations extrapolated to the complete basis set combined with Rice-Ramsperger-Kassel-Marcus and radiationless transition theories

Ab initio CCSD(T) calculations of intermediates and transition states on the singlet and triplet C3H2 potential energy surfaces extrapolated to the complete basis set limit are combined with statistical computations of energy-dependent rate constants of the C(3P)+C2H2 reaction under crossed molecular beam conditions. Rice-Ramsperger-Kassel-Marcus theory is applied for isomerization and dissociation steps within the same multiplicity and radiationless transition and nonadiabatic transition state theories are used for singlet-triplet intersystem crossing rates. The calculated rate constants are utilized to predict product branching ratios. The results demonstrate that, in qualitative agreement with available experimental data, c-C3H+H and C3+H2 are the most probable products at low collision energies, whereas l-C3H+H becomes dominant at higher Ec above approximately 25 kJ/mol.     

Theory of the photodissociation of ozone in the Hartley continuum: potential energy surfaces, conical intersections, and photodissociation dynamics

Ab initio potential energy and transition dipole moment surfaces are presented for the five lowest singlet even symmetry electronic states of ozone. The surfaces are calculated using the complete active space self consistent field method followed by contracted multireference configuration interaction (MRCI) calculations. A slightly reduced augmented correlation consistent valence triple-zeta orbital basis set is used. The ground and excited state energies of the molecule have been computed at 9282 separate nuclear geometries. Cuts through the potential energy surfaces, which pass through the geometry of the minimum of the ground electronic state, show several closely avoided crossings. Close examination, and higher level calculations, very strongly suggests that some of these seemingly avoided crossings are in fact associated with non-symmetry related conical intersections. Diabatic potential energy and transition dipole moment surfaces are created from the computed ab initio adiabatic MRCI energies and transition dipole moments. The transition dipole moment connecting the ground electronic state to the diabatic B state surface is by far the strongest. Vibrational-rotational wavefunctions and energies are computed using the ground electronic state. The energy level separations compare well with experimentally determined values. The ground vibrational state wavefunction is then used, together with the diabatic B<--X transition dipole moment surface, to form an initial wavepacket. The analysis of the time-dependent quantum dynamics of this wavepacket provides the total and partial photodissociation cross sections for the system. Both the total absorption cross section and the predicted product quantum state distributions compare well with experimental observations. A discussion is also given as to how the observed alternation in product diatom rotational state populations might be explained.     

Determination of conformational free energies of peptides by multidimensional adaptive umbrella sampling

We improve the multidimensional adaptive umbrella sampling method for the computation of conformational free energies of biomolecules. The conformational transition between the alpha-helical and beta-hairpin conformational states of an alanine decapeptide is used as an example. Convergence properties of the weighted-histogram-analysis-based adaptive umbrella sampling can be improved by using multiple replicas in each adaptive iteration and by using adaptive updating of the bounds of the umbrella potential. Using positional root-mean-square deviations from structures of the alpha-helical and beta-hairpin reference states as reaction coordinates, we obtained well-converged free energy surfaces of both the in-vacuum and in-solution decapeptide systems. From the free energy surfaces well-converged relative free energies between the two conformational states can be derived. Advantages and disadvantages of different methods for obtaining conformational free energies as well as implications of our results in studying conformational transitions of proteins and in improving force field are discussed.     

Exciton multiplication and relaxation dynamics in quantum dots: applications to ultrahigh-efficiency solar photon conversion

Huge amounts of carbon-free energy will be required during the coming decades in order to stabilize atmospheric CO2 to acceptable levels. Solar energy is the largest source of non-carbonaceous energy and can be used to produce both electricity and fuel. However, the ratio of the areal cost to the conversion efficiency for devices converting solar photons to electricity or fuel must be reduced by at least 1 order of magnitude from the present values; this requires large increases in the cell efficiency and large reductions in the cost per unit area. We have shown how semiconductor quantum dots may greatly increase photon conversion efficiencies by producing multiple excitons from a single photon. This is possible because quantization of energy levels in quantum dots slows the cooling of hot excitons, promotes multiple exciton generation, and lowers the photon energy threshold for this process. Quantum yields of 300% for exciton formation in PbSe quantum dots have been reported at photon energies 3.8 times the HOMO-LUMO transition energy, indicating the formation of three excitons/photon for all photoexcited quantum dots. Similar high quantum yields have also been reported for PbS quantum dots. A new model for this effect that is based on a coherent superposition of multiple excitonic states has been proposed.     

Photoisomerization and thermal isomerization of arylazoimidazoles

Photoisomerization and thermal isomerization behaviors of an extensive series of arylazoimidazoles are investigated. Absorption spectra are characterized by a structured pipi* absorption band around 330-400 nm with a tail on the lower energy side extending to 500 nm corresponding to an npi* transition. The trans-to-cis photoisomerization occurs on excitation into these absorption bands. The quantum yields are dependent on the excitation wavelength, as observed for azobenzene derivatives, but are generally larger than those of azobenzene. The thermal cis-to-trans isomerization rates are also generally larger than that of azobenzene and are comparable to those of 4-N,N-dimethylaminoazobenzene and 4-nitroazobenzene. Arylazoimidazoles with no substituent on the imidazole nitrogen are unique in that the quantum yield for the trans-to-cis photoisomerization and the rate of thermal cis-to-trans isomerization are particularly large. It is proposed that the fast thermal isomerization is due to an involvement of self-catalyzed and protic molecule-assisted tautomerization to a hydrazone form.     

Wave function delocalization and large-amplitude vibrations of helium on corrugated aromatic microsurfaces: tetracene.He and pentacene.He van der Waals complexes

We report accurate quantum three-dimensional calculations of highly excited intermolecular vibrational states of the van der Waals (vdW) complexes tetracene.He and pentacene.He in the S1 excited electronic state. The aromatic molecules were taken to be rigid and the intermolecular potential energy surfaces (IPESs) were modeled as a sum of atom-atom Lennard-Jones pair potentials. The IPESs are corrugated in the direction of the long (x) axis of the aromatic molecules, due to the presence of the symmetrically equivalent global double minimum for tetracene.He, and a triple minimum (central global minimum and two equivalent local minima) for pentacene.He, on each side of the aromatic plane. Both IPESs have two additional minor equivalent local minima further away from the center of the molecule. The vdW vibrational states analyzed in this work cover about 80% of the well depths of the IPESs. The mode coupling is generally weak for those states whose out-of-plane (z) mode is unexcited. However, the z-mode fundamental is strongly coupled to the short-axis (y) in-plane mode, so that the pure z-mode excitation could not be identified. The He atom exhibits large in-plane spatial delocalizaton already in the ground vdW vibrational state, which increases rapidly upon the excitation of the in-plane x and y modes, with little hindrance by the corrugation of the aromatic microsurfaces. For the vdW vibrational energies considered, the He atom spatial delocalization reaches Deltax and Deltay values of approximately 5 and 4 A, respectively, and is limited only by the finite size of the aromatic substrates. Side-crossing delocalization of the wave functions on both sides of the molecular plane is found at excitation energies >30 cm(-1), giving rise to the energy splittings of the pairs of states symmetric/antisymmetric with respect to the aromatic plane; the splittings show strong vdW vibrational mode specificity.     

Communication: Multi-state analysis of the OCS ultraviolet absorption including vibrational structure

The first absorption band of OCS (carbonyl sulfide) is analyzed using potential energy surfaces and transition dipole moment functions of the lowest four singlet and the lowest four triplet states. Excitation of the 2 (1)A' state is predominant except at very low photon energies. It is shown that the vibrational structures in the center of the band are due to excitation of the 2 (3)A' triplet state, whereas the structures at very low energies are caused by bending excitation in the potential wells of states 2 (1)A' and 1 (1)A'.     

Theoretical studies on the structures and reactivity of stannylenoids I.The structures and isomerization of stannylenoid H_2SnLiF

The structures of singlet stannylenoid H2SnLiF have been examined by ab initio MO theory. Four equilibrium states and three transition states of isomerization reaction are located. The calculation shows that the p-complex 1 is the most stable and experimentally detectable. The other three species, three-membered ring 2, o-complex 3 and tetrahedron 4, are also local minima on the potential energy surface, but are higher in energy.     

Nonadiabatic effects on peptide vibrational dynamics induced by conformational changes

Quantum dynamical simulations of vibrational spectroscopy have been carried out for glycine dipeptide (CH(3)-CO-NH-CH(2)-CO-NH-CH(3)). Conformational structure and dynamics are modeled in terms of the two Ramachandran dihedral angles of the molecular backbone. Potential energy surfaces and harmonic frequencies are obtained from electronic structure calculations at the density functional theory (DFT) [B3LYP/6-31+G(d)] level. The ordering of the energetically most stable isomers (C(7) and C(5)) is reversed upon inclusion of the quantum mechanical zero point vibrational energy. Vibrational spectra of various isomers show distinct differences, mainly in the region of the amide modes, thereby relating conformational structures and vibrational spectra. Conformational dynamics is modeled by propagation of quantum mechanical wave packets. Assuming a directed energy transfer to the torsional degrees of freedom, transitions between the C(7) and C(5) minimum energy structures occur on a sub-picosecond time scale (700...800 fs). Vibrationally nonadiabatic effects are investigated for the case of the coupled, fundamentally excited amide I states. Using a two state-two mode model, the resulting wave packet dynamics is found to be strongly nonadiabatic due to the presence of a seam of the two potential energy surfaces. Initially prepared adiabatic vibrational states decay upon conformational change on a time scale of 200...500 fs with population transfer of more than 50% between the coupled amide I states. Also the vibrational energy transport between localized (excitonic) amide I vibrational states is strongly influenced by torsional dynamics of the molecular backbone where both enhanced and reduced decay rates are found. All these observations should allow the detection of conformational changes by means of time-dependent vibrational spectroscopy.     

Derivation of class II force fields. VIII. Derivation of a general quantum mechanical force field for organic compounds

A class II valence force field covering a broad range of organic molecules has been derived employing ab initio quantum mechanical "observables." The procedure includes selecting representative molecules and molecular structures, and systematically sampling their energy surfaces as described by energies and energy first and second derivatives with respect to molecular deformations. In this article the procedure for fitting the force field parameters to these energies and energy derivatives is briefly reviewed. The application of the methodology to the derivation of a class II quantum mechanical force field (QMFF) for 32 organic functional groups is then described. A training set of 400 molecules spanning the 32 functional groups was used to parameterize the force field. The molecular families comprising the functional groups and, within each family, the torsional angles used to sample different conformers, are described. The number of stationary points (equilibria and transition states) for these molecules is given for each functional group. This set contains 1324 stationary structures, with 718 minimum energy structures and 606 transition states. The quality of the fit to the quantum data is gauged based on the deviations between the ab initio and force field energies and energy derivatives. The accuracy with which the QMFF reproduces the ab initio molecular bond lengths, bond angles, torsional angles, vibrational frequencies, and conformational energies is then given for each functional group. Consistently good accuracy is found for these computed properties for the various types of molecules. This demonstrates that the methodology is broadly applicable for the derivation of force field parameters across widely differing types of molecular structures. Copyright 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1782-1800, 2001     

Energies and spatial features for the rotationless bound states of 4He3+(2Sigmag+): a cationic core from helium cluster ionization

Ab initio quantum calculations have been carried out on the helium ionic trimer. The potential energy surface is accurately fitted, especially in the vicinity of the three equivalent minima. The spectrum of bound states for the zero angular momentum is computed and analyzed in detail. Energies and wave functions reveal several interesting features related to the fact that He3+ represents one of the few homonuclear ionic trimers that are linear in their ground vibrational state. At low energies, the triply degenerate eigenfunctions are localized at the potential minimum. With growing excitation energy, however, the wave functions exhibit stronger spatial delocalization.