Ground-state Barrier Research Articles

Photoisomerization mechanism of iminoguanidinium receptors from spectroscopic methods and quantum chemical calculations.

The hydrazone functional group, when coupled with a pyridyl substituent, offers a unique class of widely tunable photoswitches, whose E-to-Z photoisomerization equilibria can be controlled through intramolecular hydrogen bonding between the N-H hydrazone donor and the pyridyl acceptor. However, little is known about the photoisomerization mechanism in this class of compounds. To address this issue, we report a pyridine-appended iminoguanidinium photoswitch that is functionally related to acylhydrazones and provides insight into the photoisomerization processes between the E and Z configurations. The E-to-Z photoisomerization of the E-2-pyridyl-iminoguanidinium cation (2PyMIG) in DMSO, prepared as the bromide salt, was quantified by 1H NMR, and probed in real time with ultrafast laser spectroscopy. The photoisomerization process occurs on a picosecond timescale, resulting in low fluorescence yields. The multiconfigurational reaction path found with the growing string method features a small barrier (4.3 or 6.5 kcal mol-1) that the E isomer in the π-π* state must overcome to reach the minimum energy conical intersection (MECI) connecting the E and Z isomers of 2PyMIG. While two possible pathways exist depending on the orientation of the pyridine ring, both exhibit the same qualitative features along the path and at their MECIs, involving simultaneous changes in the CCNN and CNNC dihedral angles. Furthermore, the ground state barrier for pyridine ring rotation is readily accessible, thus a low barrier pathway to the experimentally observed Z isomer exists for both MECIs leading to a transition from the E isomer to photoproduct. Combining multiconfigurational reaction path calculations using growing string method with time-resolved fluorescence spectroscopy provided crucial insights into the photoisomerization process of 2PyMIG, resulting in both the computational and experimental results pointing to rapid photoisomerization via a surface crossing between the singlet π-π* and the ground states.

Theoretical Investigations on the Hydroxyl-Initialized Oxidation of Hexafluoro-2-butyne in the Presence of Oxygen.

Hexafluoro-2-butyne (C4F6) is a potential eco-friendly alternative gas in plasma, refrigerants, and electrical insulation applications. Mechanisms for the reactions of C4F6 with OH/O2 have been revealed in detail using various theoretical methods including ROCBS-Q, RCCSD(T), multireference RS2C, and extrapolations to the complete basis-set limit with Aug-cc-pVnZ (n = T, Q, 5) basis sets. Rate coefficients and product branching ratios were predicted for a wide range of temperatures and pressures using the solution of master equations. The vibrationally adiabatic ground-state barrier for the initial C4F6 + OH association was best estimated to be 1.53-2.26 kcal/mol. Energetically preferable decomposition paths for the conformation-dependent C4F6OH adducts include six-center HF elimination, four-center proton migration, and C-C bond cleavage, but the collisional deactivation is dominant under ambient conditions. The subsequent oxidation of C4F6OH by O2 bifurcates in two orientations and proceeds without any well-defined barrier followed by the successive isomerization/elimination steps, forming perfluorobiacetyl to regenerate OH radicals or trifluoroacetic acid with trifluoroacetyl radicals. The OH-recycling path accounts for a branching ratio of 70% under ambient conditions. Theoretical rate coefficients are in good agreement with the available experimental results. The effect of fluorination on the reactivity of alkynes toward OH/O2 is discussed.

An experimental and theoretical study of the Ã(2)A(″)Π-X̃(2)A(') band system of the jet-cooled HBBr/DBBr free radical.

The electronic spectra of the HBBr and DBBr free radicals have been studied in depth. These species were prepared in a pulsed electric discharge jet using a precursor mixture of BBr3 vapor and H2 or D2 in high pressure argon. Transitions to the electronic excited state of the jet-cooled radicals were probed with laser-induced fluorescence and the ground state energy levels were measured from the single vibronic level emission spectra. HBBr has an extensive band system in the red which involves a linear-bent transition between the two Renner-Teller components of what would be a (2)Π state at linearity. We have used high level ab initio theory to calculate potential energy surfaces for the bent (2)A' ground state and the linear Ã(2)A(″)Π excited state and we have determined the ro-vibronic energy levels variationally, including spin orbit effects. The correspondence between the computed and experimentally observed transition frequencies, upper state level symmetries, and H and B isotope shifts was used to make reliable assignments. We have shown that the ground state barriers to linearity, which range from 10 000 cm(-1) in HBF to 2700 cm(-1) in BH2, are inversely related to the energy of the first excited (2)Σ ((2)A') electronic state. This suggests that a vibronic coupling mechanism is responsible for the nonlinear equilibrium geometries of the ground states of the HBX free radicals.

Reactant zero-point energy is needed to access the saddle point in molecular dynamics calculations of the association reaction H + C2D2 → C2D2H∗

We report classical (CT) and quasiclassical (QCT) trajectory calculations of the association reaction H+C2D2→C2D2H∗, using an ab initio global potential energy surface. The QCT threshold is roughly 4kcal/mol, in very good agreement with the vibrationally adiabatic ground-state barrier. In contrast, the 0 and 300K CT threshold energies are roughly 10 and 8kcal/mol, respectively. These contrasting results are analyzed in detail as functions of the impact parameter and collision energy, and are of potential significance for general molecular dynamics simulations, which typically do not include zero-point energy of the reactants.

Quantum Chemistry Behind Bioimaging: Insights from Ab Initio Studies of Fluorescent Proteins and Their Chromophores

The unique properties of green fluorescent protein (GFP) have been harnessed in a variety of bioimaging techniques, revolutionizing many areas of the life sciences. Molecular-level understanding of the underlying photophysics provides an advantage in the design of new fluorescent proteins (FPs) with improved properties; however, because of its complexity, many aspects of the GFP photocycle remain unknown. In this Account, we discuss computational studies of FPs and their chromophores that provide qualitative insights into mechanistic details of their photocycle and the structural basis for their optical properties. In a reductionist framework, studies of well-defined model systems (such as isolated chromophores) help to understand their intrinsic properties, while calculations including protein matrix and/or solvent demonstrate, on the atomic level, how these properties are modulated by the environment. An interesting feature of several anionic FP chromophores in the gas phase is their low electron detachment energy. For example, the bright excited ππ* state of the model GFP chromophore (2.6 eV) lies above the electron detachment continuum (2.5 eV). Thus, the excited state is metastable with respect to electron detachment. This autoionizing character needs to be taken into account in interpreting gas-phase measurements and is very difficult to describe computationally. Solvation (and even microsolvation by a single water molecule) stabilizes the anionic states enough such that the resonance excited state becomes bound. However, even in stabilizing environments (such as protein or solution), the anionic chromophores have relatively low oxidation potentials and can act as light-induced electron donors. Protein appears to affect excitation energies very little (<0.1 eV), but alters ionization or electron detachment energies by several electron volts. Solvents (especially polar ones) have a pronounced effect on the chromophore's electronic states; for example, the absorption wavelength changes considerably, the ground-state barrier for cis-trans isomerization is reduced, and fluorescence quantum yield drops dramatically. Calculations reveal that these effects can be explained in terms of electrostatic interactions and polarization, as well as specific interactions such as hydrogen bonding. The availability of efficient computer implementations of predictive electronic structure methods is essential. Important challenges include developing faster codes (to enable better equilibrium sampling and excited-state dynamics modeling), creating algorithms for properties calculations (such as nonlinear optical properties), extending standard excited-state methods to autoionizing (resonance) states, and developing accurate QM/MM schemes. The results of sophisticated first-principle calculations can be interpreted in terms of simpler, qualitative molecular orbital models to explain general trends. In particular, an essential feature of the anionic GFP chromophore is an almost perfect resonance (mesomeric) interaction between two Lewis structures, giving rise to charge delocalization, bond-order scrambling, and, most importantly, allylic frontier molecular orbitals spanning the methine bridge. We demonstrate that a three-center Hückel-like model provides a useful framework for understanding properties of FPs. It can explain changes in absorption wavelength upon protonation or other structural modifications of the chromophore, the magnitude of transition dipole moment, barriers to isomerization, and even non-Condon effects in one- and two-photon absorption.

Rotationally Resolved S1−S0 Electronic Spectra of 2,6-Diaminopyridine: A Four-Fold Barrier Problem

A comparison of the electronic properties of the nitrogen-containing rings aniline, 2-aminopyridine, and 2,6-diaminopyridine (26DAP) shows that the potential energy surface of the molecule is significantly affected as more nitrogen atoms are added to the system. High resolution, rotationally resolved spectra of four vibrational bands in the S(1)-S(0) electronic transition of 26DAP were obtained in order to explain these changes. The zig-zagging inertial defects point to a double minimum excited state potential energy surface along the coupled amino group inversion vibrational mode, which becomes a four-fold well (and barrier) problem when the existence of two nearly degenerate isomers is taken into account. Assuming that the molecules are in the lower energy, opposite-side configuration, ab initio calculations were performed using the MP2/6-31G** level of theory to create a potential energy surface modeling the simultaneous antisymmetric NH(2)-inversion mode. The calculated potential energy surface shows a ground electronic state barrier to simultaneous NH(2) inversion of ~220 cm(-1), and a fit to experimental vibrational energy level spacings and relative intensities produces an excited electronic state barrier of ~400 cm(-1). The ground state barrier is less than that in aniline, but the excited state barrier is larger.

Environmental effects on luminescence of meso-tetra-2-chlorophenylporphyrin

Effects of solvent polarity on the photophysical behaviour of meso-tetra-2-chlorophenylporphyrin have been studied by means of steady-state absorption and fluorescence, as well as time-resolved fluorescence techniques. A non-mirror symmetric absorption and emission spectra due to vibronic borrowing were obtained. Time-resolved fluorescence study indicated the bi-exponential decay kinetics for both the emission bands, observed in steady-state emission spectra. Such findings implied that there exists two emitting species on the photoinduced conformational excursions of the excited-state equilibrium and also that their relative contributions to emission change with solvent polarity. Monte Carlo conformational search based on force-field molecular mechanics was performed to locate equilibrium conformers in the ground state which enable evaluation of the ground-state barrier energies. This was followed by CIS and ZINDO calculations to explore the excited-state barriers.

Coupled cluster investigation on the low-lying electronic states of CuCN and CuNC and the ground state barrier to isomerization

The observation of several metal cyanides and isocyanides in interstellar space has raised much interest these molecules. Optimum molecular structures, harmonic vibrational frequencies, and dipole moments of the ground electronic states (X1Sigma+), triplet excited states, and open shell singlet excited states of CuCN and CuNC were determined using different levels of nonrelativistic and scalar relativistic (Douglas-Kroll) [Ann. Phys. 82, 89 (1979)] coupled cluster theory in conjunction with atomic natural orbital basis sets and correlation consistent basis sets. For the relativistic computations the specially contracted correlation consistent Douglas-Kroll (DK) basis sets were used. Moreover, barriers to isomerization from CuCN to CuNC were computed. The predicted structures of the X1Sigma+ state for CuCN are re(Cu-C)=1.826 A and re(C-N)=1.167 A, at the most sophisticated level of theory, the scalar relativistic DK-CCSD(T)/cc-pVQZ(DK) method. These results are in excellent agreement with the experimentally determined Cu-C bond length of 1.829 A and C-N bond distance of 1.162 A. At the same level of theory, the zero-point corrected barrier to isomerization from CuCN to CuNC is estimated to be 14.7 kcal mol(-1), and the cyanide is more stable than the isocyanide by 11.5 kcal mol(-1). For both CuCN and CuNC the 3Sigma+ state is the lowest lying excited electronic state. At the DK-CCSD/cc-pVQZ(DK) level of theory, the energetic ordering of excited states of CuCN and CuNC is X1Sigma+<a3Sigma+<b3Pi<2(1)Sigma+ approximately 3Delta<1Pi<1Delta. The variations of CN bond lengths in the optimized structures for the different electronic states and the CN stretching frequencies of the ground state and the excited states suggest that metal dpi to ligand pi charge transfer is insignificant, in contrast to previous results for isoelectronic NiCO.

Cavity Ring-Down Spectroscopy of the Torsional Motions of 1,4-Bis(phenylethynyl)benzene

The torsional motions of jet-cooled 1,4-bis(phenylethynyl)benzene (BPEB), a prototype molecular wire, were studied using cavity ring-down spectroscopy in the first UV absorption band (316-321 nm). The torsional spectrum of 1,4-bis(phenylethynyl)-2,3,5,6-tetradeuteriobenzene was also recorded in the gas phase. Both spectra were successfully simulated using simple cosine potentials to describe the torsional motions. The ground-state barrier to rotation was estimated to be 220-235 cm(-1), which is similar to that of diphenylacetylene (tolane). Complementary DFT calculations were found to overestimate the torsional barrier.

Transition state structure, energetics, and rate constants for the CH 4 + F( 2P) → CH 3 + HF reaction

The CH 4 + F( 2P) → CH 3 + HF abstraction reaction was investigated using the BH&HLYP, MP2, and CCSD(T) approaches, and two series of correlation consistent basis sets. At the CCSD(T)/cc-pVTZ level, the classical barrier height (Δ V #), and the vibrationally adiabatic ground-state barrier height ( Δ V a G # ) are equal to 1.8 and 0.5 kcal/mol, respectively. CCSD(T)/cc-pVQZ calculations give a value for the enthalpy of reaction at 0 K ( Δ H 0 0 ) of −31.5 kcal/mol (Expt. −32.1 kcal/mol). Rate constants calculated with the zero-order interpolated variational transition state (IVTST-0) method are in agreement with experiment. The activation energy computed as local two-points slopes of Arrhenius plots in the temperature range of 200–400 K, equal to 0.59 kcal/mol, is also in good agreement with experiment (0.53 kcal/mol).

Coherent Raman Spectra of the ν1 Mode of Carbon Suboxide

High-resolution (0.001 cm(-1)) coherent anti-Stokes Raman spectroscopy (CARS) has been used to study the nu1 symmetric CO stretching mode of the quasi-linear molecule carbon suboxide, C3O2. Q-branch transitions are seen that originate from the ground state and from thermally populated levels of the nu7 CCC bending mode, which is of unusually low frequency. The intensity variation of the Q-branch features on cooling to about 120 K in a jet expansion requires the reversal of the order of assignment given in a previous Raman study at low resolution. The identification of the nu1 sigma(g)+ <-- sigma(g)+ transition from the ground state is confirmed by the absence of J(odd) Q-branch lines in the resolved CARS spectrum. Analysis of this band in terms of a quasi-linear model gives a good fit to the observed transitions and leads to vibrational-rotational parameters (in cm(-1)) of nu1 = 2199.9773(12) and (B' - B'') = -2.044(6) x 10(-4). Other transitions originating from higher nu7 levels occur at only slightly lower wavenumber values and permit the calculation of the double minimum potential in the Q7 bending coordinate. The results indicate that the ground-state barrier to linearity (21.5 cm(-1)) increases by only 0.6 cm(-1) when the CO symmetric stretch is excited.

A theoretical study of the potential energy surface for the reaction OH+CO→H+CO 2

Stationary points on the OH+CO→H+CO 2 potential energy surface are calculated using an extrapolated full coupled-cluster/complete basis set (FCC/CBS) method. The trans-HOCO intermediate is found to lie 30.10 kcal/mole below the OH + CO dissociation limit. For the forward reaction, the vibrationally adiabatic ground-state barrier height is predicted to be 1.03 kcal/mole. Finally, a many-body expansion potential energy surface for HOCO is obtained by fitting to the new ab initio results.

An Interpolated ab Initio Quantum Scattering Study of the Temperature Dependence of the CH3 + HBr → CH4 + Br Reaction

An interpolated ab initio quantum scattering (AIQS) study for the CH3 + HBr → CH4 + Br reaction is presented. The ab initio calculation of energy points has been done using the UMP2/6-311G(3df,d,p) level of theory. Interpolation between the energy points was done using a recently developed generalized discrete variable representation (GDVR) approach. The quantum scattering calculations were performed using a reduced dimensionality rotating line umbrella (RLU) model. The UMP2 results give a vibrationally adiabatic ground-state barrier height of 0.69 kcal/mol for the forward reaction. An unstable van der Waals complex CH3···HBr was also obtained. This complex plays only a minor role in the reaction dynamics. Calculated thermal rate coefficients show a strong nonlinear Arrhenius behavior. Below 550 K they have a negative temperature dependence, whereas a positive activation energy was obtained at higher temperatures. It was found that placing one quantum of energy in the vibrational mode of the H−Br bond str...

Quantum dynamics of the reaction of hydrogen atom with methane

Time-independent quantum scattering calculations on the H+ CH 4 → H 2+ CH 3 reaction have been performed by using a four-dimensional rotating bond umbrella (RBU) model, based on a modified potential energy surface of Espinosa-Garcı́a and Corchado. The new surface gives a vibrationally adiabatic ground state barrier height of 14.1 kcal/mol. Calculated thermal rate constants are in good agreement with the experimental results. At room temperature the rate constant obtained is 8.16×10 −19 cm 3 molec −1 s −1 . It is found that the simple energy minimization approximation gives significantly small thermal rate constants for this reaction.

Direct ab initio quantum scattering for the H2+OH→H+H2O reaction using Møller–Plesset fourth order perturbation theory

We present a realistic ab initio quantum scattering (AIQS) calculation for the chemical reaction H2+OH→H+H2O using the rotating bond approximation (RBA), based on a dual-level MP4//SAC (the fourth order Møller–Plesset perturbation theory/scaling all correlation) method with the 6-311+G(d,p) basis set. The MP4//SAC results give a vibrationally adiabatic ground state barrier height of 0.2722 eV. Calculated thermal rate constants are in good agreement with experimental measurements.

Reaction dynamics of chlorine atom with methane: Dual-level ab initio analytic potential energy surface and isotope effects

An analytic potential energy surface for the Cl+CH4⇌HCl+CH3 reaction in C3V symmetry has been obtained by fitting to 1136 energy points from a dual-level MP2/SAC (Mo/ller–Plesset second order perturbation/scaling all correlation) calculation using the 6-311G(2d,d,p) basis set. A zero-point energy correction is made to account for all modes not explicitly treated with the time-independent quantum scattering rotating line umbrella (RLU) model, which is used for the dynamics calculations. The effective potential gives a vibrationally adiabatic ground-state barrier height of 3.36 kcal/mol and an endothermicity (0 K) of 1.19 kcal/mol for the Cl+CH4 reaction, and 4.43 kcal/mol and 2.29 kcal/mol, respectively, for Cl+CD4. Thermal rate constants, tunneling and kinetic isotope effects have been investigated in detail. Calculated differential cross sections for Cl+CD4→DCl+CD3, with reactants and products in their vibrational ground states, show that the DCl product is strongly backward scattered. Further, ground state Cl+CD4 reacts to give the CD3 product predominantly unexcited at collision energies ranging from 0.15 eV to 0.25 eV. Generally, good agreement with experimental measurements and previous theoretical work is obtained.

A four dimensional quantum scattering study of the Cl+CH4⇌HCl+CH3 reaction via spectral transform iteration

We present a quantum dynamics study of the Cl+CH4⇌HCl+CH3 reaction using a four-dimensional rotating bond umbrella (RBU) model. A semiempirical potential energy surface is employed, where the zero point energy of the modes not explicitly treated in the RBU calculations is approximately included. The potential gives a vibrationally adiabatic ground state barrier height of 3.48 kcal/mol. The calculations have been performed in hypercylindrical coordinates using a log-derivative method. A single sector hyperspherical projection method has been developed for applying boundary conditions. A guided spectral transform (GST) Krylov subspace method has been constructed to find the eigenstates of the coupling matrix appearing in the coupled channel equations. The results show that the product methyl is rotationally cold for the forward reaction. A pronounced tunneling effect on the rate constants was obtained. The calculated thermal rate constants are 12%–45% smaller than the experimental results over the temperature range 200–800 K for the Cl+CH4⇌HCl+CH3 reaction. State-to-state differential cross sections have been studied at a kinetic energy of 0.159 eV. A detailed comparison with experimental measurements is made.

The Perpendicular C–H Stretching Band ν9/ν13and the Torsional Potential of Dimethylacetylene

The perpendicular band of the fourfold degenerate C–H stretching vibration of dimethylacetylene (2-butyne) occurring in the region 2955–3065 cm−1has been measured with Doppler-limited resolution at a temperature of ∼195 K on a difference-frequency laser spectrometer, and on a high-resolution Fourier transform instrument at room temperature as well as in a molecular jet at ∼20 K. From a detailed rotational analysis of this complex band, based on an extension of the model of the rotational–torsional interactions described by P. R. Bunker and C. di Lauro (Chem. Phys.190,159–169, 1995), accurate spectroscopic constants were determined for the upper CH stretching state, along with values for the first three components of the Fourier expansion for the torsional potential in the ground state, and for six components of this potential in the upper state. Over 700 lines assigned to 37 well-resolved subbands plus 25 additional unresolved line-likeQ-branches were fitted with an overall standard deviation of 0.0024 cm−1. The results yield a value of 6.316 ± 0.034 cm−1for the barrier to internal rotation in the ground state, and 6.643 ± 0.006 cm−1for the C–H stretching state. This value for the ground state barrier is somewhat higher than that recently determined from an analysis of the CH3rocking band by P. R. Bunkeret al.(J. Mol. Spectrosc.162,142–151, 1993).

Theoretical study of some 1,3-substituted (1,3-diketonato)borondifluorides. Potential energy curve relevant to the barrier crossing reaction

Ab initio Hartree-Fock calculations utilising STO-3G, 3-21G ∗ and 6-31G ∗ basis sets have been performed on three neutral and highly polar molecules, (diformylmethine)borondifluoride, (acetylacetonato)borondifluoride and (dibenzylmethine) borondifluoride. The calculated and experimental structures are well correlated when using the HF/3-21G ∗ basis set, except for the structure parameters involving the boron atom. The HF/6-31G ∗ basis set does not improve the accuracy in structure calculations. The conformational analysis is in agreement with the experimentally observed C 2v symmetrical structures, where the boron atom is tetrahedrally coordinated. The calculations support a one-dimensional ground state barrier crossing reaction for (dibenzylmethine)borondifluoride, where the phenyl torsion is the most likely reaction coordinate. Both HF/6-31G ∗ calculations and the second-order Møller-Plesset correction with the 3-21G ∗ basis set suggest an activation energy of the ground state reaction of about 30 kJ mol −1. The ground state barrier crossing reaction kinetics is evaluated by the Kramers theory. The calculated ground state parameters relevant to the barrier crossing reaction are compared with the experimentally observed excited state values.

The ICN-INC system: experiment and quantum chemical calculations

Photolysis of ICN in an argon matrix leads to the formation of INC, identified by the appearance of three infrared absorption bands. The assignment is confirmed by comparing the vibrational frequencies and absorption band intensities with good quality ab initio calculations. The endothermicity of the isomerization reaction and the ground state barrier to INC formation is also computed. The good agreement between theory and experiment demonstrates the use of quantum chemical calculation as an analytical tool and highlights the partnership of experiment and theory in chemical research.