Two-dimensional Potential Energy Surface Research Articles

Conformational analysis of N-methylformamide in ground S0 and excited S1 and T1 electronic states

For conformers of the N-methylformamide (HCONHCH3) molecule, calculations of equilibrium geometry parameters, harmonic vibration frequencies, energy differences and potential barriers to conformational transitions were performed in the ground (S0) and lowest excited singlet (S1) and triplet (T1) electronic states. In the S0 state, the molecule exists in trans and cis stable conformations (having Cs symmetry). Our calculations show that the electronic excitations T1←S0 and S1←S0 cause changes in the structure of conformers: both HCON and HNCC fragments become pyramidal and rotate around the CN bond. As a result, in each excited electronic state under consideration, there are 12 minima forming six pairs of equivalent conformers separated by relatively small potential barriers. One- and two-dimensional potential energy surface sections corresponding to different intramolecular large-amplitude motions were calculated using the MP2/aug-cc-pVTZ (S0) and CASPT2/cc-pVTZ (S1 and T1) methods. Anharmonic vibrational problems for large-amplitude motions were solved, and the corresponding frequencies were estimated.

Charge density of the biologically active molecule (2-oxo-1,3-benzoxazol-3(2H)-yl)acetic acid.

(2-Oxo-1,3-benzoxazol-3(2H)-yl)acetic acid is a member of a biologically active class of compounds. Its molecular structure in the crystal has been determined by X-ray diffraction, and its gas phase structure was obtained by quantum chemical calculations at the B3LYP/6-311++G(d,p) level of theory. In order to understand the dynamics of the molecule, two presumably soft degrees of freedom associated with the relative orientation of the planar benzoxazolone system and its substituent at the N atom were varied systematically. Five conformers have been identified as local minima on the resulting two-dimensional potential energy surface within an energy window of 27 kJ mol(-1). The energetically most favourable minimum closely matches the conformation observed in the crystal. Based on high-resolution diffraction data collected at low temperature, the experimental electron density of the compound was determined. Comparison with the electron density established by theory for the isolated molecule allowed the effect of intermolecular interactions to be addressed, in particular a moderately strong O-H...O hydrogen bond with a donor...acceptor distance of 2.6177 (9) Å: the oxygen acceptor is clearly polarized in the extended solid. The hydrogen bond connects consecutive molecules to chains, and the pronounced charge separation leads to stacking between neighburs with antiparallel dipole moments perpendicular to the chain direction.

Hindered rotor tunneling splittings: an application of the two-dimensional non-separable method to benzyl alcohol and two of its fluorine derivatives.

In this work we present a novel application of the two-dimensional non-separable (2D-NS) method to the calculation of torsional tunneling splittings in systems with two hindered internal rotors. This method could be considered an extension of one-dimensional methods for the case of compounds with two tops. The 2D-NS method includes coupling between torsions in the kinetic and potential energy. Specifically, it has been applied to benzyl alcohol (BA) and two of its fluorine derivatives: 3-fluorobenzyl alcohol (3FBA) and 4-fluorobenzyl alcohol (4FBA). These molecules present two torsions, i.e., about the -CH2OH (ϕ1) and -OH (ϕ2) groups. The electronic structure calculations to build the two-dimensional torsional potential energy surface were performed at the DF-LMP2-F12//DF-LMP2/cc-pVQZ level of theory. For BA and 4FBA the calculated ground-state vibrational level splittings are 429 and 453 MHz, respectively, in good agreement with the experimental values of 337.10 and 492.82 MHz, respectively. In these two cases there are four equivalent wells and the tunneling splitting is the result of transitions between the two closer minima along ϕ1. The analysis of the wavefunctions, as well as the previous experimental work on the system, supports this conclusion. For 3FBA the observed ground-state splitting is 0.82 MHz, whereas in this case the calculated value amounts only to 0.02 MHz. The 2D-NS method, through the analysis of the wavefunctions, shows that this tiny tunneling splitting occurs between the two most stable minima of the potential energy surface. Additionally, we predict that the first vibrationally excited tunneling splitting will also be small and exclusively due to the interconversion between the second lowest minima.

Atropisomerization of 8-Membered Dibenzolactam: Experimental NMR and Theoretical DFT Study.

Detailed experimental and theoretical quantum mechanical analysis of the atropisomerization mechanism of a complex, bridged biaryl molecule with imbedded biphenyl, amine, and lactam moieties, 7,8-diallyl-5-benzyl-7,8-dihydrodibenzo[e,g][1,4]diazocin-6(5H)-one (1), was undertaken. Experimental Gibbs free activation energy, activation enthalpy, and activation entropy were established by temperature-dependent kinetic NMR experiments. Theoretical analysis utilized density functional theory (DFT) calculations at the B3LYP/6-31G(d) level of theory. Twelve energy minima and 17 transition states associated with five different atropisomer interconversion pathways were found by the combination of DFT calculated two-dimensional potential energy surfaces (2D PES) and the quadratic synchronous transit-guided (QST2) method. Among the five possible atropisomerization pathways, the lowest Gibbs free activation energy 25.8 kcal/mol was in close agreement with the experimentally determined value of 26.8 kcal/mol. Theoretical activation entropies and enthalpies were also consistent with experimental data. Geometrical and vibrational analysis of transition states and metastable intermediates suggested the mechanism of atropisomer interconversion of 1 as a rotation of the eclipsed endocyclic coordinate in a clockwise or counterclockwise direction along the ring. Puckering ability at least in one of the segments of the ring appears to be one of the most critical factors defining the height of atropisomerization barrier.

Theoretical Spectroscopic Characterization at Low Temperatures of Dimethyl Sulfoxide: The Role of Anharmonicity.

The structural and spectroscopic parameters of dimethyl sulfoxide (DMSO) are predicted from CCSD(T)-F12 calculations that can help to resolve the outstanding problem of the rovibrational spectroscopy. DMSO is a near oblate top that presents a trigonal pyramidal geometry. Rotational parameters are determined at the equilibrium and in selected vibrational states. For the ground state, the rotational constants were calculated to be A0 = 7031.7237 MHz, B0 = 6920.1221 MHz, and C0 = 4223.3389 MHz, at few megahertz from the previous experimental measurements. Ab initio calculations allow us to assert that DMSO rotational constants are strongly dependent on anharmonic effects. Asymmetry increases with the vibrational energy. Harmonic frequencies, torsional parameters, and a two-dimensional potential energy surface (2D-PES) focused to describe the internal rotation of the two methyl groups are determined at the CCSD(T)-F12 level of theory. For the medium and small amplitude motions, anharmonic effects are estimated with MP2 theory getting an excellent agreement with experimental data for the ν11 and ν23 fundamentals. Torsional energies and transitions are computed variationally form the 2D-PES that denotes strong interactions between both internal tops. The vibrationally corrected V3 torsional barrier is evaluated to be 965.32 cm(-1). The torsional splitting of the ground vibrational state has been estimated to be lower than 0.01 cm(-1). Although the ν13 torsional fundamental is found at 229.837 cm(-1) in good agreement with previous assessment, there is not accord for the low intense transition ν24. A new assignment predicting ν24 to lie between 190 and 195 cm(-1) is proposed.

Dynamics of H Atom Production from Photodissociation of Acetic Acid-d(1).

Detailed dissociation dynamics of H(D) from acetic acid-d1 (CH3COOD) has been investigated upon electronic excitation to the (1)(n,π*), S1 state at 205 nm by measuring laser-induced fluorescence spectra of the fragment H(D) atoms. In addition, quantum yields for the H(D) atom dissociation channels, CH3COO + D and CH2COOD + H, were measured, which are 0.07 ± 0.03 and 0.17 ± 0.03, respectively. From the Doppler broadened spectra, the center-of-mass translational energy releases into products were obtained. To determine the detailed dissociation dynamics, two-dimensional potential energy surfaces along the reaction coordinate including the coordinate directly coupled to the dissociation coordinate were examined by employing quantum chemical calculations. For the CH3COO + D channel, the coupled coordinate is the dihedral angle of D against the COO plane. The dissociation of D(H) from acetic acid should take place along the triplet surface via surface crossing from the initially excited S1 state. Along the triplet surface, an exit channel barrier exists, which originates from the structural difference between the T1 and the product asymptotes, especially the dihedral angle of D against the COO plane. The observed translational energy releases were successfully estimated by the barrier impulsive model based upon the calculated two-dimensional potential energy surfaces at the B3LYP/cc-pVDZ level of theory.

Modeling of dexmedetomidine conformers and their interactions with alpha2 adrenergic receptor subtypes

Dexmedetomidine (4-[(S)-1-(2,3-dimethyl-phenyl)-ethyl]-1H-imidazole), Dex, is potent agonist acting on α2-adrenergic receptors (α2-ARs). It can exist at the physiological pH in both forms: neutral and protonated. The results of receptor-independent and receptor-dependent studies applied to both forms of Dex are reported. A conformational analysis with PM3 semiempirical MO and ab initio HF/6-31G* methods was carried out for both forms of Dex. The calculated geometries of low-energy conformers of Dex were compared with X-ray geometry and those of conformers resulted from molecular docking of Dex in the binding pockets of 3D homology models of the α2A-, α2B-, and α2C-adrenoceptor subtypes. A MM/QM (molecular mechanics/quantum mechanics) docking study was performed to refine and optimize receptor–ligand complex and close contacts between the ligand and amino acids lining the binding cavity. Two-dimensional potential energy surface and docking results suggest that the imidazole ring can easily adopt the best orientation for an efficient interaction with the carboxylate group of Asp3.32 from the binding cavity of alpha2 adrenergic receptor subtypes.

Potential energy surfaces for anion states of 5-chlorouracil

SynopsisWe present two-dimensional potential energy surfaces for the negative ions states π1*, π2* and σCCI* of the potential radiosensetizer 5-chlorouracil. These were built along the C–Cl stretching mode (reactive coordinate) and an out-of-plane angular displacement of Cl atom (tuning coordinate), as obtained from scattering calculations performed with the Schwinger multichannel method. Analysis of the potential energy surfaces and quantum nuclear dynamics support that chloride elimination arises from an indirect mechanism around 1.5 eV, where the incoming electron is captured into a π* orbital and is then transfered to the dissociative σCCI* orbital.

Reduced-Dimensionality Semiclassical Transition State Theory: Application to Hydrogen Atom Abstraction and Exchange Reactions of Hydrocarbons

Quantum mechanical methods for calculating rate constants are often intractable for reactions involving many atoms. Semiclassical transition state theory (SCTST) offers computational advantages over these methods but nonetheless scales exponentially with the number of degrees of freedom (DOFs) of the system. Here we present a method with more favorable scaling, reduced-dimensionality SCTST (RD SCTST), that treats only a subset of DOFs of the system explicitly. We apply it to three H abstraction and exchange reactions for which two-dimensional potential energy surfaces (PESs) have previously been constructed and evaluated using RD quantum scattering calculations. We differentiated these PESs to calculate harmonic frequencies and anharmonic constants, which were then used to calculate cumulative reaction probabilities and rate constants by RD SCTST. This method yielded rate constants in good agreement with quantum scattering results. Notably, it performed well for a heavy-light-heavy reaction, even though it does not explicitly account for corner-cutting effects. Recent extensions to SCTST that improve its treatment of deep tunneling were also evaluated within the reduced-dimensionality framework. The success of RD SCTST in this study suggests its potential applicability to larger systems.

Cyanides/isocyanides abundances in the interstellar medium – IV. Temperature dependence of SiCN/SiNC rate coefficients and astrophysical applications

Accurate determination of collisional rate coefficients is an essential step in the estimation of the SiCN and SiNC abundances in the interstellar and circumstellar media. In this paper, we carry out calculations of rate coefficients for the rotational (de-)excitation of SiCN and SiNC molecules in collision with He. The calculations are based on new two-dimensional potential energy surfaces obtained from highly correlated ab initio calculations. Coupled-States quantum approximation was used in the scattering calculations to obtain collisional (de-)excitation cross-sections of SiCN and SiNC by He. The spin–orbit coupling and Λ-doublet splitting of SiCN and SiNC levels were taken into account explicitly. Rate coefficients for transitions among the first 92 rotational levels of SiCN and SiNC were calculated for temperatures ranging from 5 to 100 K. Moderate differences exist between the rate coefficients of both isomers. Subsequently, the new collisional data are used to simulate the excitation of SiCN and SiNC in the circumstellar gas. We obtain the brightness and excitation temperatures of selected lines frequently observed towards the circumstellar envelopes and we find that local thermodynamic equilibrium conditions are not fulfilled for these species. Radiative transfer calculations are then needed in order to accurately determine their abundances. Our results also show that previous estimations of the cyanides/isocyanides abundance ratios were incorrect and the present calculations show that SiCN, the most stable isomer, is more abundant than SiNC. This shows again the evidence of selective cyanide chemistry.

Microwave Spectrum of Hexafluoroisopropanol and Torsional Behavior of Molecules with a CF3-C-CF3 Group.

This paper presents the first microwave spectroscopic investigation on hexafluoroisopropanol (HFIP). A pulsed nozzle Fourier transform microwave spectrometer has been used to determine the rotational constants for HFIP as A = 2105.12166(18) MHz, B = 1053.99503(12) MHz, and C = 932.33959(13) MHz. In addition, five isotopologues of HFIP have been observed experimentally to determine the accurate structure of HFIP. The observed spectrum could be assigned to the most stable conformer of HFIP, called antiperiplanar. Available spectroscopic information and ab initio calculations on five prototype molecules helped in exploring the torsional behavior of molecules having a CF3-C-CF3 group. Two-dimensional potential energy surfaces have been analyzed for all molecules, which explained the presence/absence of doubling in the rotational transitions. With the help of natural bond orbital (NBO) analysis, reasons for the conformational preference of HFIP have been explained.

Excited-state ring-opening mechanism of cyclic ketones: a MS-CASPT2//CASSCF study.

We have employed complete active space self-consistent field (CASSCF) and its second-order perturbation (MS-CASPT2) methods to study the S1 and T1 excited-state ring-opening mechanisms and S1 excited-state deactivation channels of cyclopropanone, cyclobutanone, cyclopentanone, and cyclohexanone. On the basis of optimized minima, transition states, conical intersections, refined energies, and relaxed two-dimensional S1 and T1 potential energy surfaces, we find that, with the ring-strain decrease from cyclopropanone to cyclohexanone, (1) the ring-opening S1 and T1 barrier increases from 0.0 and 0.0 to 19.7 and 10.4 kcal/mol, respectively; (2) the electronic state responsible for the dominant ring-opening reaction varies from the S1 state of cyclopropanone to the T1 state of cyclopentanone and cyclohexanone; and (3) the S1 ring opening gradually becomes inefficient even blocked in cyclopentanone and cyclohexanone. This work shows that these dissimilar excited-state dynamics could originate from different ring strain of small cyclic ketones.

High-Resolution Millimeter Wave Spectroscopy and Ab Initio Calculations of Aminomalononitrile

The HCN trimer aminomalononitrile (H2NCH(CN)2, AMN) is considered as a key compound in prebiotic chemistry and a potential candidate for detection in the interstellar medium. In this view, we studied the rotational spectrum of AMN in the 120-245 GHz frequency range. The spectroscopic work was augmented by high-level ab initio calculations. The calculations showed that between two existing rotamers, symmetric and asymmetric, the most stable is the asymmetric conformation, and it is the only conformation observed in the recorded spectra. The symmetric conformation is 6.7 kJ/mol higher in energy and thus has a very low Boltzmann factor. The analysis of the rotational spectra of the A conformation has shown that the observed lines exhibit a doublet or quartet structure owing to two large-amplitude motions, C-N torsion and amino group inversion. To study the large-amplitude motions in detail, we calculated a two-dimensional potential energy surface and determined the barrier heights for the torsion and inversion, Vt = 12.5 kJ/mol and Vi = 19.1 kJ/mol. About 2500 assigned rotational transitions in the ground vibrational state were fitted within experimental accuracy using the reduced axes system Hamiltonian. The set of obtained spectroscopic parameters allows accurate calculation of transition frequencies and intensities for an astrophysical search of AMN.

Complexation of allyl radicals and hydrochloric acid in helium nanodroplets.

Infrared spectra of the allyl radical-HCl complex in superfluid helium nanodroplets have been recorded in the IR frequency range of 2750-3120 cm(-1). Six fundamental bands were observed, five of which have been assigned to the C-H stretch vibrations of the allyl radical. No additional CH bands were observed upon the binding of HCl. The band at 2800.3 cm(-1) can unambiguously be assigned to the bound HCl stretch, which is red-shifted by 106 cm(-1) compared to that of the free HCl. Stark spectra and pickup curves were recorded and support our assignment. In accompanying ab initio calculations, we found four equivalent minima and computed a two-dimensional potential energy surface for the HCl positioning on the allyl radical plane at the CCSD(T)/TZVPP level. Based on our findings, we conclude that the ground-state structure of the complex shows two energetically equivalent T-shaped minimum structures. Because of small barriers between the two minima, a delocalization of the HCl is anticipated.

High-level QM/MM calculations support the concerted mechanism for Michael addition and covalent complex formation in thymidylate synthase.

Thymidylate synthase (TS) is a promising cancer target, due to its crucial function in thymine synthesis. It performs the reductive methylation of 2'-deoxyuridine-5'-phosphate (dUMP) to thymidine-5'-phosphate (dTMP), using N-5,10-methylene-5,6,7,8-tetrahydrofolate (mTHF) as a cofactor. After the formation of the dUMP/mTHF/TS noncovalent complex, and subsequent conformational activation, this complex has been proposed to react via nucleophilic attack (Michael addition) by Cys146, followed by methylene-bridge formation to generate the ternary covalent intermediate. Herein, QM/MM (B3LYP-D/6-31+G(d)-CHARMM27) methods are used to model the formation of the ternary covalent intermediate. A two-dimensional potential energy surface reveals that the methylene-bridged intermediate is formed via a concerted mechanism, as indicated by a single transition state on the minimum energy pathway and the absence of a stable enolate intermediate. A range of different QM methods (B3LYP, MP2 and SCS-MP2, and different basis sets) are tested for the calculation of the activation energy barrier for the formation of the methylene-bridged intermediate. We test convergence of the QM/MM results with respect to size of the QM region. Inclusion of Arg166, which interacts with the nucleophilic thiolate, in the QM region is important for reliable results; the MM model apparently does not reproduce energies for distortion of the guanidinium side chain correctly. The spin component scaled-Møller-Plessett perturbation theory (SCS-MP2) approach was shown to be in best agreement (within 1.1 kcal/mol) while the results obtained with MP2 and B3LYP also yielded acceptable values (deviating by less than 3 kcal/mol) compared with the barrier derived from experiment. Our results indicate that using a dispersion-corrected DFT method, or a QM method with an accurate treatment of electron correlation, increases the agreement between the calculated and experimental activation energy barriers, compared with the semiempirical AM1 method. These calculations provide important insight into the reaction mechanism of TS and may be useful in the design of new TS inhibitors.

Structural Dependence of Electronic Properties in A-A-D-A-A-Type Organic Solar Cell Material

Small conjugated molecules (SCMs) are promising candidates for organic photovoltaic (OPV) devices because of their structural simplicity, well control over synthetic reproducibility, and low purification cost. However, industrial development of SCM-based OPV devices requires improving their performance, which in turn relies on the fundamental understanding of structural dependence of electronic properties of SCMs. Herein, we report the structural and electronic properties of the BCNDTS molecule as a model system for acceptor-acceptor-donor-acceptor-acceptor (A-A-D-A-A) type SCMs, using density functional theory (DFT) and time-dependent DFT methods. Systematic calculations of two-dimensional potential energy surfaces, molecular electrostatic potential surfaces, ground state frontier molecular orbital energies, and the vertical excitation energies are performed. We found that the lowest energy conformation of the BCNDTS molecule is planar. The planar conformation favors the lowest ground state and the excited state energies as well as the strongest oscillator strength. The present results suggest that SCMs containing central dithienosilole cores connected with 2,1,3-benzothiadiazole groups have potential to be an efficient electron donor for OPV devices.

Vibrational spectra, theoretical calculations, and two-dimensional potential energy surface for the ring-puckering vibrations of 2,4,7-trioxa[3.3.0]octane.

2,4,7-Trioxa[3.3.0]octane (247TOO) is an unusual bicyclic molecule which can exist in four different conformational forms which are determined by the directions of the two ring- puckering motions. The vibrational assignments of 247TOO have been made based on its infrared and Raman spectra and theoretical density functional theory (DFT) calculations. The two ring-puckering motions (in-phase and out-of-phase) were observed in the Raman spectra of the liquid at 249 and 205 cm(-1) and these values correspond well to the DFT values of 247 and 198 cm(-1). Ab initio calculations were utilized to calculate the structures and conformational energies for the four energy minima and the barriers to interconversion and the data was utilized to generate a two-dimensional potential energy surface (PES) for the two ring-puckering motions. The resulting quantum state energies for this PES were then calculated in order to better understand the patterns that are produced when the PES has four energy minima at different energy values. The wave functions corresponding to the different quantum states were also calculated. The NMR spectrum of 247TOO showed the presence of the two lowest energy conformations, consistent with the results of the ab initio calculations.

Photoisomerization mechanism of 1,1′-dimethyl-2,2′-pyridocyanine in the gas phase and in solution

The trans→cis and cis→trans photoisomerization mechanisms of 1,1′-dimethyl-2,2′-pyridocyanine have been investigated theoretically in the gas phase and in methanol. Two-dimensional potential energy surfaces were computed for the ground and first excited singlet states of the isolated molecule using complete active space self-consistent field method. Our computations suggest that the torsion around the central CC bonds with carbon-out-of-plane motion is the preferred photoisomerization mechanism. In the gas phase, conical intersections were found near the minima of excited state. The excited-state decay follows a barrierless minimum-energy pathway before the molecule moves to the excited-state global minimum (minS1) and the system relaxes to the ground state through a conical intersection. In methanol, the system would first reach a stationary structure of C2 symmetry after the trans form is electronically excited. Solvent polarity effects were investigated in chloroform, dichloromethane, 1-propanol, ethanol, methanol, and water. There is a significant barrier between the stationary structure of C2 symmetry and minS1 in the excited state in high polarity solvents. Thus, Me-1122P has a much longer lifetime of the excited state in solvents of high polarity.

Quantum dynamics of the abstraction reaction of H with cyclopropane.

The dynamics of the abstraction reaction of H atoms with the cyclopropane molecule is studied using quantum mechanical scattering theory. The quantum scattering calculations are performed in hyperspherical coordinates with a two-dimensional (2D) potential energy surface. The ab initio energy calculations are carried out with CCSD(T)-F12a/cc-pVTZ-F12 level of theory with the geometry and frequency calculations at the MP2/cc-pVTZ level. The contribution to the potential energy surface from the spectator modes is included as the projected zero-point energy correction to the ab initio energy. The 2D surface is fitted with a 29-parameter double Morse potential. An R-matrix propagation scheme is carried out to solve the close-coupled equations. The adiabatic energy barrier and reaction enthalpy are compared with high level computational calculations as well as experimental data. The calculated reaction rate constants shows very good agreement when compared with the experimental data, especially at lower temperature highlighting the importance of quantum tunnelling. The reaction probabilities are also presented and discussed. The special features of performing quantum dynamics calculation on the chemical reaction of a cyclic molecule are discussed.

Some remarks on the model of the extended gentlest ascent dynamics

The study of molecular systems involves models describing the evolution of the system through barriers separating basins of attraction on a high dimensional potential energy surface. It is a challenge problem inherent to a complex molecular system. Recently Samanta and E (J Chem Phys 136:124104, 2012) have proposed an extended gentlest ascent dynamics where the system should hop from one saddle point on a potential energy surface to a next saddle point. In the present study we do an analysis of this dynamical model using different two-dimensional potential energy surfaces. The extended gentlest ascent dynamics is a model that corresponds in its mathematical formulation to a set of first order ordinary differential equations. Due to this fact the initial conditions and features are also studied to see their effect on the dynamical behavior.