Torsional Barrier Research Articles

Performance of Density-Functional Tight-Binding in Comparison to Ab Initio and First-Principles Methods for Isomer Geometries and Energies of Glucose Epimers in Vacuo and Solution.

Density functional theory (DFT) is a widely used methodology for the computation of molecular and electronic structure, and we confirm that B3LYP and the high-level ab initio G3B3 method are in excellent agreement for the lowest-energy isomers of the 16 glucose epimers. Density-functional tight-binding (DFTB) is an approximate version of DFT with typically comparable accuracy that is 2 to 3 orders of magnitude faster, therefore generally very suitable for processing large numbers of complex structures. Conformational isomerism in sugars is well known to give rise to a large number of isomer structures. On the basis of a comprehensive study of glucose epimers in vacuo and aqueous solution, we found that the performance of DFTB is on par to B3LYP in terms of geometrical parameters excluding hydrogen bonds and isomer energies. However, DFTB underestimates both hydrogen bonding interactions as well as torsional barriers associated with rotations of the hydroxy groups, resulting in a counterintuitive overemphasis of hydrogen bonding in both gas phase as well as in water. Although the associated root mean squared deviation from B3LYP within epimer isomer groups is only on the order of 1 kcal/mol, this deviation affects the correct assignment of major isomer ordering, which span less than 10 kcal/mol. Both second- as well as third-order DFTB methods are exhibiting similar deviations from B3LYP. Even after the inclusion of empirical dispersion corrections in vacuum, these deviations remain for a large majority of isomer energies and geometries when compared to dispersion-corrected B3LYP.

Self-Organization and Charge Transport Properties of Selenium and Tellurium Analogues of Polythiophene.

A series of conjugated polymers comprising polythiophene, polyselenophene, and polytellurophene with branched 3,7-dimethyloctyl side chains, well-matched molecular weight, dispersity, and regioregularity is synthesized. The ionization potential is found to vary from 5.14 to 5.32 eV, with polytellurophene having the lowest potential. Field-effect transistors based on these materials exhibit distinct hole transport mobility that varies by nearly three orders of magnitude, with polytellurophene having the highest mobility (2.5 × 10-2 cm² V-1 s-1 ). The large difference in mobility demonstrates the significant impact of heteroatom substitution. Although the series of polymers are very similar in structure, their solid-state properties are different. While the thin film microstructure of polythiophene and polyselenophene is identical, polytellurophene reveals globular features in the film topography. Polytellurophenes also appear to be the least crystalline, even though their charge transport properties are superior to other samples. The torsional barrier and degree of planarity between repeat units increase as one moves down group-16 elements. These studies show how a single atom in a polymer chain can have a substantial influence on the bulk properties of a material, and that heavy group-16 atoms have a positive influence on charge transport properties when all other variables are kept unchanged.

Reduced Free Energy Perturbation/Hamiltonian Replica Exchange Molecular Dynamics Method with Unbiased Alchemical Thermodynamic Axis.

Replica-exchange molecular dynamics (REMD) has been proven to efficiently improve the convergence of free-energy perturbation (FEP) calculations involving considerable reorganization of their surrounding. We previously introduced the FEP/(λ,H)-REMD algorithm for ligand binding, in which replicas along the alchemical thermodynamic coupling axis λ were expanded as a series of Hamiltonian boosted replicas along a second axis to form a two-dimensional replica-exchange exchange map [Jiang, W.; Roux, B., J. Chem. Theory Comput. 2010, 6 (9), 2559-2565]. Aiming to achieve a similar performance at a lower computational cost, we propose here a modified version of this algorithm in which only the end-states along the alchemical axis are augmented by boosted replicas. The reduced FEP/(λ,H)-REMD method with one-dimensional unbiased alchemical thermodynamic coupling axis λ is implemented on the basis of generic multiple copy algorithm (MCA) module of the biomolecular simulation program NAMD. The flexible MCA framework of NAMD enables a user to design customized replica-exchange patterns through Tcl scripting in the context of a highly parallelized simulation program without touching the source code. Two Hamiltonian tempering boosting scheme were examined with the new algorithm: a first one based on potential energy rescaling of a preidentified "solute" and a second one via the introduction of flattening torsional free-energy barriers. As two illustrative examples with reliable experiment data, the absolute binding free energies of p-xylene and n-butylbenzene to the nonpolar cavity of the L99A mutant of T4 lysozyme were calculated. The tests demonstrate that the new protocol efficiently enhances the sampling of torsional motions for backbone and side chains around the binding pocket and accelerates the convergence of the free-energy computations.

Probing the methyl torsional barriers of the doubly substituted methyl-ethyl Criegee intermediate by FTMW spectroscopy

In a previous work, Cabezas et al., 2017 [21], we reported the rotational study of the doubly substituted methyl-ethyl Criegee intermediate, C2H5C(CH3)OO, by using Fourier transform microwave spectroscopy. Four different conformers were found showing A/E splittings due to the internal rotation of methyl tops. However for one of the conformers, syn2, some of the observed lines showed additional splitting that could not be assigned. The present work has been aimed to shed light on these transition line splittings of the syn2 conformer which are assigned to additional splittings coming from the two nonequivalent tops. As a consequence, 182 lines have been observed and the analysis of the internal rotation motions of two non-equivalent methyl tops enabled us to determine the barrier heights of the hindered methyl rotation of the two tops.

Acetyl Methyl Torsion in Pentan-2-one As Observed by Microwave Spectroscopy.

The rotational spectra of two conformers of pentan-2-one (also known as methyl propyl ketone) were recorded in the frequency range from 2 to 40 GHz using two molecular jet Fourier transform microwave spectrometers. Fine splittings due to the internal rotations of the acetyl methyl group CH3CO- and the butyryl methyl group -COCH2CH2CH3 were resolved and analyzed with high accuracy. The torsional barriers of the acetyl and the butyryl methyl groups are 238.14 and 979 cm-1, respectively, for the lowest energy conformer, as well as 188.384 and 1032 cm-1, respectively, for the other one. From the results obtained for the acetyl methyl group, a general rule to predict its torsional barrier in ketones based on the molecular symmetry is proposed.

Atomistic Model of Realistic Crystalline Mesoporous Organosilica Materials Including Nanochannels

The new class of periodic mesoporous organosilica materials (PMOs), due to the peculiar features, has attracted growing interest from several research areas. We present an atomistic model of a p-phenylenesilica crystalline mesoporous structure with a hexagonal framework, explicitly including channels on nanoscale. OPLS-AA force-field optimization, to get a suitable PMO structure compared with the experimental one, is described. In particular, DFT calculations have been performed to calculate torsional energy barrier of phenyl rings connected to the silicon atoms belonging to inorganic layers and to improve the OPLS-AA force field performances for these materials. Finally, inclusion of small molecules and their interactions with PMO walls have been investigated for CO2 and H2O.

FT-IR and Raman Spectroscopy and Computation of 5-Methylfurfural

5-Methylfurfural (5MF) was studied by vibrational (IR and Raman) spectroscopy and computational methods (DFT/B3LYP&MP2). FT-IR and FT-Raman spectra in KBr (at room temperature) were collected. The Gaussian 09 and Spartan 08 programs were used for conformational analysis and calculations of molecular structure, torsional barrier, and vibrational spectral data for the 5MF molecule. The obtained results were used in the analysis of experimental vibrational spectra of 5MF molecule.

Reservoir pH replica exchange.

We present the reservoir pH replica exchange (R-pH-REM) method for constant pH simulations. The R-pH-REM method consists of a two-step procedure; the first step involves generation of one or more reservoirs of conformations. Each reservoir is obtained from a standard or enhanced molecular dynamics simulation with a constrained (fixed) protonation state. In the second step, fixed charge constraints are relaxed, as the structures from one or more reservoirs are periodically injected into a constant pH or a pH-replica exchange (pH-REM) simulation. The benefit of this two-step process is that the computationally intensive part of conformational search can be decoupled from constant pH simulations, and various techniques for enhanced conformational sampling can be applied without the need to integrate such techniques into the pH-REM framework. Simulations on blocked Lys, KK, and KAAE peptides were used to demonstrate an agreement between pH-REM and R-pH-REM simulations. While the reservoir simulations are not needed for these small test systems, the real need arises in cases when ionizable molecules can sample two or more conformations separated by a large energy barrier, such that adequate sampling is not achieved on a time scale of standard constant pH simulations. Such problems might be encountered in protein systems that exploit conformational transitions for function. A hypothetical case is studied, a small molecule with a large torsional barrier; while results of pH-REM simulations depend on the starting structure, R-pH-REM calculations on this model system are in excellent agreement with a theoretical model.

Femtosecond Time-Resolved Raman Spectroscopy Reveals Structural Evidence for meta Effect in Stilbenols.

The meta effect in substituted aromatics plays a crucial role in their excited-state photophysical properties. Meta-substituted hydroxyarenes such as naphthols, stilbenols, and chromophoric constituents of green fluorescent proteins show unusual photoacidity and enhanced fluorescence lifetime and quantum yield when compared to their para-derivatives. Variation in the excited state features of the meta-derivatives when compared to the para-derivatives in stilbenols has been attributed to the enhanced torsional barrier for interconversion between the planar and the twisted perpendicular forms. Herein, we employed femtosecond time-resolved Raman spectroscopy to provide the direct structural evidence for the enhanced torsional barrier in meta-stilbenol. The Raman band profiles of the olefinic C═C stretch related to the torsional motion are found to decay with time constants of ∼750 and ∼13 ps in meta-stilbenol and para-stilbenol respectively, unraveling the structural evidence for the observed enhanced photoacidity originating from enhanced rates of excited-state proton transfer. Further, time-resolved fluorescence measurements are performed to elucidate the relaxation pathways of the excited states of the stilbenols.

FTIR synchrotron spectroscopy of the S–H stretching fundamental of the 12CH332SH species of methyl mercaptan

ABSTRACTThe infrared Fourier transform spectrum of the S–H stretching fundamental band of 12CH332SH has been recorded using synchrotron radiation at the far-infrared beamline of the Canadian Light Source in Saskatoon. The S–H stretch is a hybrid band predominantly of perpendicular b-type with a small parallel a-component. With both ΔK = +1 and ΔK = −1 sub-bands present, the assignments are well determined from ground-state combination difference relations. The identified sub-bands access S–H stretching ground torsional substates from K′ = 0–14 for A and E torsional species. The substate origins have been obtained by expanding the term values in J(J + 1) power series, and have been fitted to a simple 6-parameter Fourier Hamiltonian to deduce the torsional energies. The oscillation amplitude of the S–H stretching torsional curves is 0.547 cm−1 compared to 0.653 cm−1 for the ground state, implying an increase on the order of 6.9% in the torsional barrier height. The vibrational wavenumber for the S–H stretch mode is found to be 2603.5 cm−1.

Conformational effects on the torsional barriers in m-methylanisole studied by microwave spectroscopy

The microwave spectrum of m-methylanisole (also known as 3-methylanisole, or 3-methoxytoluene) was measured using a pulsed molecular jet Fourier transform microwave spectrometer operating in the frequency range of 2-26.5 GHz. Quantum chemical calculations predicted two conformers with the methoxy group in trans or cis position related to the ring methyl group, both of which were assigned in the experimental spectrum. Due to the internal rotation of the ring methyl group, all rotational transitions introduced large A-E splittings up to several GHz, which were analyzed with a newly developed program, called aixPAM, working in the principal axis system. There are significant differences in the V3 potential barriers of 55.7693(90) cm-1 and 36.6342(84) cm-1 determined by fitting 223 and 320 torsional components of the cis and the trans conformer, respectively. These values were compared with those found in other m-substituted toluenes as well as in o- and p-methylanisole. A comparison between the aixPAM and the XIAM code (using a combined axis system) was also performed.

A Possible Progenitor of the Interstellar Sulfide Bond: Rovibrational Characterization of the Hydrogen Disulfide Cation HSSH+

Abstract S2H (HSS) has been observed very recently in the interstellar medium, specifically in the Horsehead nebula. The protonated form, S2H2 +, is believed to be a necessary intermediate in its creation in the gas phase in UV-irradiated regions. However, little is known about this radical cation. This work showcases that the trans-HSSH+ isomer is 0.12 eV lower in energy than the cis with a 1.05 eV upper limit to the torsional rotation barrier. Additionally, the vibrational frequencies and rotational constants for both structures are provided in full here for the first time. The cis isomer is likely the more detectable since it possesses a permanent dipole moment and has a high-intensity vibrational frequency for the antisymmetric H−S−S bend at 926 cm−1 (10.8 μm), in the heart of the mid-IR spectral range. A third isomer, H2S−S+ is also reported herein lying ∼0.9 eV in energy above trans-HSSH+. This isomer could play a role in the formation of S2H since it would be kinetically favored in the reaction of sulfur cations with hydrogen sulfide. Further assessment of this third, higher-energy isomer is left for future work.

Theoretical Study of Infrared Spectra of OCS-( pH2)2, OCS-( oD2)2, OCS-(HD)2, and Mixed OCS- pH2-He Trimers.

The calculated rovibrational energy levels and infrared spectra for OCS-( pH2)2, OCS-( oD2)2, OCS-(HD)2 and mixed OCS- pH2-He trimers are obtained by performing the exact basis-set calculations for the first time based on the newly developed potential energy surfaces ( J. Chem. Phys. 2017, 147, 044313). The "adiabatic-hindered-rotor" (AHR) method is used for reduced-dimension treatment of the hydrogen rotation. The predicted band origin shifts and the infrared spectra are in good agreement with the available experimental values: for the band origin shifts and infrared transitions, the root-mean-square(rms) deviations are smaller than 0.044 and 0.002 cm-1, respectively. We extend the assignments to the unrecorded infrared transitions for OCS-( pH2)2 and OCS-(HD)2 complexes and identify the infrared spectra for OCS-( oD2)2 and OCS- pH2-He for the first time. Three-dimensional density distributions for the ground states of OCS-( pH2)2, OCS- pH2-He, and OCS-(He)2 show that the pH2 molecules are localized in their corresponding global minimum regions, while the pronounced locations of the He atoms are missing in OCS- pH2-He and OCS-(He)2 with forming incomplete circles around the OCS axis. A clear tunneling splitting is observed for the torsional motion of the two hydrogen molecules ( pH2, HD, or oD2) on a ring about the OCS molecular axis, whereas no tunneling splitting is found in OCS- pH2-He or OCS-(He)2 due to a much lower torsional barrier.

Substituent control of the ultrafast twisted intramolecular charge transfer rate in dimethylaminochalcone derivatives.

The effect of acceptor strength variation on ultrafast twisting relaxation dynamics was investigated by comparing the ultrafast relaxation dynamics in a series of dimethylaminochalcone (DMAC) derivatives. Employing femtosecond resolved transient absorption and fluorescence experiments, the twisted intramolecular charge transfer (TICT) relaxation rate is shown to vary from 2.0 picoseconds in a weak electron accepting system to 420 femtoseconds in a strong electron accepting system. The strength of the acceptor, empirically expressed as Hammett's constant, is shown to exhibit a linear free energy relationship (LFER) with the twisting rate. It is proposed that variation in the charge pulling capacity of the acceptor modifies the torsional barrier along the TICT coordinate in the S1 state, resulting in a tunable TICT relaxation rate, depending on the acceptor strength.

Toward Fractioning of Isomers through Binding-Induced Acceleration of Azobenzene Switching.

The E/Z isomerization process of a uracil-azobenzene derivative in which the nucleobase is conjugated to a phenyldiazene tail is studied in view of its ability to form triply H-bonded complexes with a suitably complementary 2,6-diacetylamino-4-pyridine ligand. UV-vis and 1H NMR investigations of the photochemical and thermal isomerization kinetics show that the thermal Z → E interconversion is 4-fold accelerated upon formation of the H-bonded complex. DFT calculations show that the formation of triple H-bonds triggers a significant elongation of the N═N double bond, caused by an increase of its πg* antibonding character. This results in a reduction of the N═N torsional barrier and thus in accelerated thermal Z → E isomerization. Combined with light-controlled E → Z isomerization, this enables controllable fractional tuning of the two configurational isomers.

The torsional barriers of two equivalent methyl internal rotations in 2,5-dimethylfuran investigated by microwave spectroscopy

The microwave spectrum of 2,5-dimethylfuran was recorded using two pulsed molecular jet Fourier transform microwave spectrometers which cover the frequency range from 2 to 40 GHz. The internal rotations of two equivalent methyl tops with a barrier height of approximately 439.15 cm−1 introduce torsional splittings of all rotational transitions in the spectrum. For the spectral analysis, two different computer programs were applied and compared, the PAM-C2v-2tops code based on the principal axis method which treats several torsional states simultaneously, and the XIAM code based on the combined axis method, yielding accurate molecular parameters. The experimental work was supplemented by quantum chemical calculations. Two-dimensional potential energy surfaces depending on the torsional angles of both methyl groups were calculated and parametrized.

Torsional Barriers to Rotation and Planarization in Heterocyclic Oligomers of Value in Organic Electronics.

In order to understand the conformational behavior of organic components in organic electronic devices, we have computed the torsional potentials for a library of thiophene-based heterodimers. The accuracy and efficiencies of computational methods for these organic materials were benchmarked for 11 common density functionals with three Pople basis sets against a Focal Point Analysis (FPA) on a model oligothiophene 2,5-bis(3-tetradecylthiophen-2-yl)thieno[3,2-b]-thiophene (BTTT) system. This study establishes a set of general trends in regards to conformational preferences, as well as planarization and rotational barriers for a library comprised of common fragments found in organic materials. These gas phase structures are compared to experimental crystal structures to determine the effect of crystal packing on geometry. Finally, we analyze the structure of hole-transporting material DERDTS-TBDT and design a new oligomer likely to be planar in the solid state.

Way to Highly Emissive Materials: Increase of Rigidity by Introduction of a Furan Moiety in Co-Oligomers

Rigid linear organic co-oligomers are prospective materials for organic optoelectronics. In this work, we explored intramolecular factors affecting the torsional rigidity and its influence on optoelectronic properties of the alternating furan/phenylene and thiophene/phenylene co-oligomers in both ground and first singlet excited states. Furan/phenylene co-oligomer exhibits almost twice higher torsional rigidity than its thiophene analog. Effect of intramolecular O…H and S…H interactions on torsional barriers was found to be negligible as compared with the conjugation efficiency. The higher torsional rigidity of furan and thiophene co-oligomers has been proven to be reflected in the fine-structure of the UV-Vis absorption spectrum of the former. The increase of furan co-oligomer rigidity as compared with its thiophene analog lowers reorganization energy for hole, electron and exciton transfer. Remarkably the substitution of thiophene by furan almost 20 times lowers reorganization energy for exciton transfe...

Thermodynamic properties of pyrrole, 1-methylpyrrole, 2,4-dimethylpyrrole, and 2,5-dimethylpyrrole: Experimental and computational results

New measurements of critical temperature, saturated liquid heat capacity from temperature T≈315K to T≈550K, and saturated liquid density from T=323K to T≈475K are reported for pyrrole (Chemical Abstracts registry number [109-97-7]), 1-methylpyrrole [96-54-8], 2,4-dimethylpyrrole [625-82-1], and 2,5-dimethylpyrrole [625-84-3]. New measurements of vapor pressure are reported for 2,4-dimethylpyrrole {338<(T/K)<477} and 2,5-dimethylpyrrole {341<(T/K)<479}, as well as the enthalpy of combustion determined with oxygen-bomb calorimetry for 2,4-dimethylpyrrole. These new measurements are combined with literature values to calculate thermodynamic properties in the ideal-gas state for extended ranges of temperature for all compounds: pyrrole {298<(T/K)<550}, 1-methylpyrrole {298<(T/K)<530}, 2,4-dimethylpyrrole {298<(T/K)<600}, and 2,5-dimethylpyrrole {298<(T/K)<560}. Molar thermodynamic functions (enthalpies, entropies, and Gibbs energies) for the liquid and ideal-gas states were derived from the experimental studies at selected temperatures. Statistical calculations were performed with optimized geometries, scaled vibrational frequencies, and methyl rotational potentials performed using B3LYP hybrid density functional theory with the def2-TZVPPD basis set. Methyl torsional barriers were evaluated at the DLPNO-CCSD(T)/def2-QZVP level of theory using the B3LYP/def2-TZVPPD geometries. Computed ideal-gas properties are shown to be in excellent accord with ideal-gas entropies derived from thermophysical property measurements, as well as with reported experimental heat capacities for the ideal-gas state. All experimental results are compared with property values available in the literature.

Conformational Switching of HOCO Radical: Selective Vibrational Excitation and Hydrogen-Atom Tunneling.

Conformers of carboxyl radical (HOCO) have been studied by IR spectroscopy in argon and nitrogen matrices. In an argon matrix, only the lower-energy conformer trans-HOCO is observed, whereas both cis and trans conformers are found for deuterated carboxyl radical DOCO. In a nitrogen matrix, both conformers of HOCO and DOCO isotopologues can be prepared, indicating strong stabilization of the higher-energy cis conformer by a nitrogen matrix. Selective vibrational excitation promotes the trans-to-cis and cis-to-trans conversions of DOCO in an argon matrix and HOCO and DOCO in a nitrogen matrix, which is the first conformational photoswitching of an open-shell species. In a nitrogen matrix, the cis-to-trans and trans-to-cis conversions of HOCO is also found upon broadband IR light of the spectrometer, and the ratio of the quantum yields of these processes is about 3.3. The photoswitching peculiarities are in agreement with the available theoretical energy barriers. The higher-energy cis conformer decays to the lower-energy trans conformer via hydrogen-atom tunneling through the torsional barrier, which is also a unique observation for an open-shell species. The tunneling mechanism of the cis-to-trans switching is supported by the low-temperature limit of the reaction rate and by the H/D kinetic isotope effect. Our results suggest a large difference in the H/D kinetic isotope effects in nitrogen and argon matrices (∼5 and >100, respectively). The stabilizing effect on cis-DOCO by a nitrogen matrix (by 2 orders of magnitude versus an argon matrix) is much smaller than that on cis-HOCO (estimated to be >104).