Cis Transition Research Articles

Amide isomerization pathways: Electronic and structural background of protonation- and deprotonation-mediated cis-trans interconversions.

The cis-trans isomerization of amide bonds leads to wide range of structural and functional changes in proteins and can easily be the rate-limiting step in folding. The trans isomer is thermodynamically more stable than the cis, nevertheless the cis form can play a role in biopolymers' function. The molecular system of N-methylacetamide · 2H2O is complex enough to reveal energetics of the cis-trans isomerization at coupled cluster single-double and coupled cluster single-double and perturbative triple [CCSD(T)] levels of theory. The cis-trans isomerization cannot be oversimplified by a rotation along ω, since this rotation is coupled with the N-atom pyramidal inversion, requesting the introduction of a second dihedral angle "α." Full f(ω,α) potential energy surfaces of the different amide protonation states, critical points and isomerization reaction paths were determined, and the barriers of the neutral, O-protonated and N-deprotonated amides were found too high to allow cis-trans interconversion at room temperature: ∼85, ∼140, and ∼110 kJ mol-1, respectively. For the N-protonated amide bond, the cis form (ω = 0°) is a maximum rather than a minimum, and each ω state is accessible for less than ∼10 kJ mol-1. Here we outline a cis-trans isomerization pathway with a previously undescribed low energy transition state, which suggests that the proton is transferred from the more favorable O- to the N-protonation site with the aid of nearby water molecules, allowing the trans → cis transition to occur at an energy cost of ≤11.6 kJ mol-1. Our results help to explain why isomerase enzymes operate via protonated amide bonds and how N-protonation of the peptide bond occurs via O-protonation.

Electronic Spectroscopy of cis- and trans-meta-Vinylbenzyl Radicals.

The D0(2A″)-D1(2A″) electronic transition of resonance-stabilized radical C9H9 isomers cis- and trans-meta-vinylbenzyl (MVB) has been investigated using resonant two-color two-photon ionization (R2C2PI) and laser-induced fluorescence. The radicals were produced in a discharge of m-vinyltoluene diluted in Ar and probed under jet-cooled conditions. The origin bands of the cis and trans conformers are at 19 037 and 18 939 cm-1, respectively. Adiabatic ionization energies near 7.17 eV were determined for both conformers from two-color ion-yield scans. Dispersed fluorescence (DF) was used to conclusively identify the cis-conformer: ground-state cis-MVB eigenvalues calculated for a Fourier series fit of a computed vinyl torsion potential are in excellent agreement with torsional transitions in the 19 037 cm-1 DF spectrum. R2C2PI features arising from cis- or trans-MVB were distinguished by optical-optical hole-burning spectroscopy and vibronic assignments were made with guidance from density functional theory (DFT) and time-dependent density functional theory (TDDFT) calculations. There is a notable absence of mirror symmetry between excitation and emission spectra for several totally symmetric modes, whereby modes that are conspicuous in emission are nearly absent in excitation, and vice versa. This effect is largely ascribed to interference between Franck-Condon and Herzberg-Teller contributions to the electronic transition moment, and its pervasiveness a consequence of the low symmetry (Cs) of the molecule, which permits intensity borrowing from several relatively bright electronic states of A″ symmetry.

Analysis of Interconversion between Atropisomers of Chiral Substituted 9,9’‐Bicarbazole

AbstractInterconversion of atropisomers of chiral 3,3’‐di‐tert‐butyl‐9,9’‐bicarbazole linked by a single N−N bond was analyzed by DFT calculations and experiments. The calculations revealed that the trans transition state has a lower energy for the interconversion than the cis transition state. The lowest transition state of interconversion between natural dixiamycins A and B containing a 9,9’‐bicarbazole structure was found to be the trans transition state. The calculations also indicated that degradation through N−N bond cleavage was faster than racemization. Atropisomeric enantiomers of 3,3’‐di‐tert‐butyl‐9,9’‐bicarbazole were resolved by chiral HPLC for the first time, and then racemization and N−N bond cleavage were investigated by heating experiments, showing that racemization did not take place below the degradation temperature.

Catalytic activity of water molecules in gas‐phase glycine dimerization

AbstractThe dimerization of glycine is the simplest oligomerization of amino acids and plays an important role in biology. Although this reaction is thermodynamically unfavorable in the aqueous phase, it has been shown to be spontaneous in the gas phase and proceeds via two different concerted reaction mechanisms known as cis and trans. This may have profound implications in prebiotic chemistry as common atmospheric prenucleation clusters are thought to have participated in gas‐phase reactions in the early Earth's atmosphere. We hypothesize that particular arrangements of water molecules in these clusters could lead to lowering of the reaction barrier of amino acid dimerization and could lead to abiotic catalysis toward polypeptides. We test our hypothesis on a system of the cis transition state of glycine dimerization solvated by one to five water molecules using a combination of a genetic algorithm‐based configurational sampling, density functional theory geometries, and domain‐based local pair natural orbital coupled‐cluster electronic structure. First, we discuss the validity of the model chemistries used to obtain our results. Then, we show that the Gibbs free energy barrier for the concerted cis mechanism can indeed be lowered by the addition of up to five water molecules, depending on the temperature.

Development of Light-Responsive Poly(γ-Benzyl-L-Glutamate) as Photo Switches by a One-Step NCA Method.

Synthesized polypeptide is attracting an increased interests due to its excellent biological characteristic and adjustable chemical properties in bio-related fields. But polypeptide itself has no switching properties, which is harmful to the development of its application as a control component. Herein, light-responsive poly(γ-benzyl-L-glutamate)s (PBLGs) is synthesized by a one-step NCA method using p-aminoazobenzene (m-AZO) and p-diaminoazobenzene (m-DAZO) as initiators. PBLGs exhibit amorphous characteristics with obvious Tg transition, which are 14°C for PBLG1 and 21°C for PBLG2. In order to forecast the structure-property information of PBLGs, theoretical UV-vis spectra as well as the energy gap between HOMO and LUMO is calculated by DFT calculation. Experimental results of UV-vis spectra exhibit similar characteristics to those of theorical UV-vis spectra except for the 40–50 nm red-shifting of absorbance peak. Furthermore, the absorbance intensities of PBLGs have a good linear relationship with their concentration, but their linearity range depending on concentration is completely different. Then, trans–cis transition under a different excitation source and cis–trans recovery in a dark environment are tracked in real-time by UV-vis spectra to evaluate the light response performances. It is found that UV light is the only effective excitation source for PBLG1, and blue light is another effective excitation source for PBLG2 besides UV light. Furthermore, the addition of alcohol and water as cosolvents has little effect on trans→cis transition in UV-light-excited systems, but it shortens recovery time of the cis→trans process in a dark environment. By contrast, the detectable isomerization process becomes unclear with the addition of alcohol in blue-light-excited system. Furthermore, either alcohol or water in solvents accelerate both the trans→cis and cis→trans process in a blue-light-excited system.

Vapor-Deposited Glasses Highlight the Role of Density in Photostability.

Photoresponsive molecules can be integrated into glassy materials to probe the local environment and invoke responsive changes in polymer behavior. For example, recent experiments and simulations have studied increased stability in vapor-deposited glasses by examining the photoisomerization rate of a probe molecule. At the theoretical level, past work relied on coarse-grained simulations to explain the role of photoisomerization on glass behavior. In order to effectively exploit these molecular probes, an ability to quantify how the local environment influences the photoisomerization rate is needed. In this work, we present all-atom molecular-dynamics (MD) simulations of molecular glasses of photoresponsive azobenzene (AB) molecules. The stability of these in-silico samples is probed using photoisomerization, where AB molecules can undergo trans → cis transition upon light exposure. Vapor-deposited and bulk-cooled glasses of AB are simulated using a classical dihedral-switching potential developed by Böckmann et al. (J. Phys. Chem. A 2010, 114, 745-754) to model the photoisomerization process. The MD simulations include thousands of molecules and run for tens of nanoseconds. These size and time scales allow us to explore the broad distribution of photoisomerization wait times, which yields two results. First, the wait-time distributions for both physical vapor deposition and bulk-cooled glasses depend strongly on sample and local density, showing that density or local packing is a primary factor in glass stability against photoisomerization and the experimentally measured photoresponse. Second, the distribution follows a power-law with exponent b ≈ 1.25-1.3 that extends to longer times with increasing density. The power-law distribution suggests a connection with previous experiments that related barriers to photoisomerization with an effective photoisomerization temperature.

Method of full discretization in joint calculation in time of the system “construction - foundation - soil”

Introduction. Prospective transition of CIS to the European design standards in the construction industry requires development of new and modification of known engineering methods for calculation and design of construction. Creation and development of such methods should be based on fundamental research that can become the basis for the development of principally new, innovative technologies. Methods. The paper consists of basis and practical application of the method of full discretization. This method is a special modification of finite element method for the solving of problems of the creep. Practical application of the method is illustrated with modeling and applied tasks. Results. The paper presents a joint calculation of the “structure - foundation - soil” system using the example of a reservoir of a modular biological wastewater treatment plant designed for filtration fields in the village of Tasboget, Akmola region, the Republic of Kazakhstan. The full picture of the evolution of the stress-strain state of structures is gained, taking into account the material creep and the history of construction. There is a comparison of result calculations with and without technology of erection of structures.

Controlling Self-Assembly with Light and Temperature.

Complexes between the anionic polyelectrolyte sodium polyacrylate (PA) and an oppositely charged divalent azobenzene dye are prepared in aqueous solution. Depending on the ratio between dye and polyelectrolyte stable aggregates with a well-defined spherical shape are observed. Upon exposure of these complexes to UV light, the trans → cis transition of the azobenzene is excited resulting in a better solubility of the dye and a dissolution of the complexes. The PA chains reassemble into well-defined aggregates when the dye is allowed to relax back into the trans isomer. Varying the temperature during this reformation step has a direct influence on the final size of the aggregates rendering temperature in an efficient way to easily change the size of the self-assemblies. Application of time-resolved small-angle neutron scattering (SANS) to study the structure formation reveals that the cis → trans isomerization is the rate-limiting step followed by a nucleation and growth process.

A Photo‐Responsive Organogel Based on Pyrene‐Substituted Acylhydrazone Derivative

AbstractA new simple pyrene‐substituted acylhydrazone derivative, 4‐(3,4‐dioctyloxy) phenyl‐1‐pyrene acylhydrazone (PAH‐8), was designed and synthesized. The PAH‐8 can form thermo‐reversible organogel in DMSO, and shows gelation‐induced enhanced fluorescence emission. Xerogel exhibits ribbon‐like fibrous aggregates with widths of 0.5‐1 μm. The PAH‐8 organogel indicates photo‐responsive behaviors due to the trans‐cis isomerizations of ‐C=N‐ bond upon exposure to visible or UV light. Upon visible light irradiation, the partial trans‐cis isomerization of the ‐C=N‐ bond causes the fiber morphology to disappear, resulting in gel‐sol transition, whereas the PAH‐8 organogel exhibits few photoisomerizations from trans to cis transition without breakage of the gel state upon UV light irradiation.

Role of trans to cis Transition in Viral Fusion Pore Dilation

Fusion of viral and host membranes is a key step during infection by membrane-enclosed viruses. The fusion pore plays a critical role, and must dilate to release the viral genome. Previous studies of fusion mediated by influenza A hemagglutinin (HA) revealed ∼2-5 nm pores that flickered before dilating to >10 nm. The mechanisms are unknown.Here we studied HA-mediated fusion pore dynamics using a novel single-pore assay, combined with computational simulations accessing extraordinarily long ms-s timescales. We measured pores between HA-expressing fibroblasts and bilayer nanodiscs. From pore currents we infer pore size with millisecond time resolution. Unlike previous in vitro studies, use of nanodiscs limited the membrane contact areas and maximum pore sizes, better mimicking the initial phases of virus-endosome fusion. With wild type (WT) HA, fusion pores flickered about a mean pore size ∼1 nm. By contrast, fusion pores formed by GPI-anchored HA nucleated at half the WT rate and were significantly larger.We developed radically coarse-grained, explicit lipid molecular dynamics simulations of the fusion pore reconstituted with post-fusion, trans HA hairpins. With WT HA, fusion pores were small, similar to experiment. Over time hairpins gradually converted from trans to cis, but contrary to a common view, cis hairpins accumulated on the “viral” membrane, not the pore waist, due to the low mobility HA transmembrane domains. With GPI-HA the anchoring lipids were far more mobile and the trans-cis transition much accelerated. Once most hairpins had converted to cis, because apposing membranes were released the fusion pore dilated significantly.Our results suggest pore dilation requires the trans-cis transition. We hypothesize that this transition is accelerated in GPI-HA by the more mobile lipid anchor, explaining the larger observed pores.

Mechanistic investigation of cis and trans oxidative addition to acetylacetonato-1,5-cyclooctadieneiridium(I)

Density functional theory (DFT) calculations of the oxidative addition of CH3I, as well as Hg(CN)2, to [Ir(acac)(cod)] are described (acac=acetylacetone). Both cis and trans oxidative addition mechanisms are considered and compared to experimental data. The DFT calculated thermodynamically most stable oxidative addition products are trans-[Ir(acac)(cod)(CH3)(I)] and cis-[Ir(acac)(cod)(HgCN)(CN)]. The steric demand of the cod ligand leads to a distorted octahedral trans-[Ir(acac)(cod)(CH3)(I)] complex, with the CCH3-Ir-I angle deviating by more than 20° from 180°, as expected for real octahedral geometry. However, the steric demand of the cod ligand does not lead to any cis transition state for the [Ir(acac)(cod)]+CH3I reaction, rather the trans transition state is energetically favoured, as is generally found for oxidative addition of CH3I to square planar complexes. On the other hand, oxidative addition of Hg(CN)2 to [Ir(acac)(cod)], occurs via a concerted three-centre cis transition state structure. The concerted three-centre cis transition state structure is confirmed by the existence of a ring critical point, as obtained by the Bader’s quantum theory of atoms in molecules analysis of the cis transition state structure. Both trans addition of CH3I to [Ir(acac)(cod)] as well as cis addition of Hg(CN)2 to [Ir(acac)(cod)], are in agreement with experimental observation.

Dynamic NMR and Quantum-Chemical Study of the Stereochemistry and Stability of the Chiral MoO2(acac)2 Complex in Solution.

The stereochemistry and dynamics of MoO2(acac)2 in benzene, chloroform, and toluene were investigated by variable temperature (1)H NMR, density functional theory (SOGGA11-X, B3LYP), and ab initio (MP2) methods. In solution, an equilibrium between two chiral enantiomers with C2 symmetry was identified, Λ-cis-MoO2(acac)2 and Δ-cis-MoO2(acac)2. The two enantiomers are connected via achiral cis transition states that switch the enantiomeric conformations via a Ray-Dutt, Bailar, and a newly described racemization twisting mechanism. All three mechanisms have similar calculated activation energies. Activation parameters Ea, ΔH(‡), and ΔS(‡) were experimentally determined for the exchange process, with a small, negative ΔS(‡), and a positive ΔH(‡) of 68.1 kJ mol(-1) in benzene, 54.9 kJ mol(-1) in chloroform, and 60.6 kJ mol(-1) in toluene, in reasonable general agreement with the calculations. Trans configurations of MoO2(acac)2 are very much higher in energy than cis and are not relevant in the temperature range experimentally studied, 243-340 K. The enantiomers interconvert within seconds near room temperature and much faster at elevated temperatures. Racemization will thus prevent the use of enantiomerically pure MoO2(acac)2 for chiral catalysis under practical conditions.

Theoretical design of visible light driven azobenzene-based photo-switching molecules

The preparation of switchable azobenzene derivatives driven by visible light is desirable for applications in biomolecular systems. o-R-substituted 4,4′-diacetamidoazobenzene derivatives (RH, CH3, OCH3 or OH) were investigated by using both density functional theory (DFT) and reactive molecular dynamics simulations. DFT calculations demonstrated that the nonplanar azo trans geometric structure, which caused by bulky groups tetra substituted in the ortho-position, is the key factor to enable the trans→cis transition with visible light. Furthermore, 100 independent reactive MD simulations demonstrated that 71% trans isomers of tetra o-OCH3-substituted 4,4′-diacetamidoazobenzene translated to cis, in good agreement with the experimental data.

A computational investigation into the substituent effect on the chemo- and stereoselectivity of crossed intermolecular radical anion [2 + 2] cycloadditions of enones

The chemoselectivity of cycloaddition is caused by the bulky group on the C atoms which form σ bond in the first step. The stereoselectivity mainly caused by the difference in steric interaction between the trans and cis transition states.

REMPI spectroscopy and theoretical calculations of cis and trans 3-fluoro-N-methylaniline

The ab initio and density functional theory (DFT) calculations of 3-fluoro-N-methylaniline (3FNMA) reveal that two rotamers, cis and trans 3FNMA, are stable for each of the S0, S1, and D0 states. The vibronic spectra of the two rotamers in the S1 state have been recorded by the one-color resonant two-photon ionization (R2PI) spectroscopy. The band origins of the S1←S0 electronic transition of cis and trans 3FNMA are found to be 33816±3 and 34023±3cm−1. The two rotamers display similar vibrational frequencies, and the slight energy difference in some modes reflects the conformation effect due to the relative orientation of the NHCH3 group. Besides, the trans rotamer displays more vibronic features in the low-frequency region, which are active modes mainly involving the CH3 and the NHCH3 groups. By the two-color R2PI spectroscopy, the adiabatic ionization energies (IEs) of cis and trans 3FNMA are determined to be 61742±10 and 61602±10cm−1, respectively. It is derived from the R2PI spectroscopic data that, compared with the trans rotamer, the cis rotamer is more stable by 302±25cm−1 in the S1 state, but less stable by 45±25cm−1 in the D0 state. With the aid of theoretical calculations, the substitution and conformation effects on the properties of 3FNMA, including the molecular structures, vibrational frequencies, and the relative stability of the two rotamers, were discussed in detail.

REMPI and MATI spectroscopic study of selected cis and trans 3-chlorostyrene rotamers

The ab initio and DFT calculations predict two stable rotamers, cis and trans, for 3-chlorostyrene in each of the S0, S1 and D0 states. In the two-color resonant two-photon ionization (2C-R2PI) spectra, the band origins of S1←S0 electronic transition of cis and trans 3-chlorostyrene appears respectively at 33766±3 and 34061±3cm−1. The mass-analyzed threshold ionization (MATI) spectra give the adiabatic ionization energies of 69701±4cm−1 and 69571±4cm−1 for cis and trans rotamers. Within the experimental detection limit, the measured transition energies are the same for both the 35Cl and 37Cl isotopomers. The observed active modes of rotamers in the S1 and D0 states involve mainly the in-plane ring deformation and substituent-sensitive bending vibration. It is derived from the 2C-R2PI and MATI spectroscopic data that the cis rotamer is more stable than the trans rotamer by 218±30, 513±30 and 88±30cm−1 for the S0, S1 and D0 states, respectively.

Photothermal studies of the room temperature photo-induced spin state change in the Fe(III)(salten)(mepepy) complex

The complex [Fe(III)(salten)(mepepy)]BPh 4 (salten = 4-azaheptamethylene-1,7-bis(salicylideneiminate; mepepy = 1-(pyridin-4-yl)-2-(N-methylpyrrol-2-yl)-ethene; BPh 4 = tetraphenyl borate) has been investigated to determine the volume and enthalpy changes associated with the room temperature photo-induced spin crossover. Here we report the photophysical properties of the trans to cis isomerization of the mepepy ligand as well as the spin crossover of the Fe(III)(salten)(mepepy) complex in acetonitrile:water mixtures using photoacoustic calorimetry (PAC). The PAC studies indicate that the trans to cis transition of the mepepy ligand occurs faster than the ∼20 ns response time of the acoustic detector and gives rise to a negligible volume change (0.7 ± 0.3 mL mol −1) and an enthalpy change of 33 ± 10 kcal mol −1. These results are consistent with the loss of a charge assisted hydrogen bond between a water molecule and the pyridyl ring of the mepepy upon photoisomerization. In the case of Fe(III)(salten)(mepepy) photoexcitation, PAC results indicate that the high-spin to low-spin transition, also occurring in ≲ 20 ns, gives rise to small volume and enthalpy changes (0.9 mL mol −1 and 4 kcal mol −1). Analysis of the results indicate that the observed thermodynamics are related to a distortion of the Fe(II)(salten)(mepepy) complex associated with the cleavage of an Fe ⋯ N bond upon spin conversion.

Silicon-based molecular switch junctions

In contrast to the static operations of conventional semiconductor devices, the dynamic conformational freedom in molecular devices opens up the possibility of using individual molecules as new types of devices such as a molecular conformational switch or for molecular data storage. Bistable molecules—such as those having two stable cis and trans isomeric configurations—could provide, once clamped between two electrodes, a switching phenomenon in the non-equilibrium current response. Here, we model molecular switch junctions formed at silicon contacts and demonstrate the potential of such tunable molecular switches in electrode/molecule/electrode configurations. Using the non-equilibrium Green function (NEGF) approach implemented with the density-functional-based tight-binding (DFTB) theory, a series of properties such as electron transmissions, current-voltage characteristics in the different isomer conformations, and potential energy surfaces (PESs) as a function of the reaction coordinates along the trans to cis transition were calculated for two azobenzene-based model compounds. Furthermore, in order to investigate the stability of molecular switches under ambient conditions, molecular dynamics (MD) simulations at room temperature were performed and time-dependent fluctuations of the conductance along the MD pathways were calculated. Our numerical results show that the transmission spectra of the cis isomers are more conductive than trans counterparts inside the bias window for both model compounds. The current voltage characteristics consequently show the same trends. Additionally, calculations of the time-dependent transmission fluctuations along the MD pathways have shown that the transmission in the cis isomers is always significantly larger than that in their trans counterparts, showing that molecular switches can be expected to work as robust molecular switching components.

Photophysical Studies of the Trans to Cis Isomerization of the Push−Pull Molecule: 1-(Pyridin-4-yl)-2-(N-methylpyrrol-2-yl)ethene (mepepy)

Organic molecules possessing intramolecular charge-transfer properties (D-pi-A type molecules) are of key interest particularly in the development of new optoelectronic materials as well as photoinduced magnetism. One such class of D-pi-A molecules that is of particular interest contains photoswitchable intramolecular charge-transfer states via a photoisomerizable pi-system linking the donor and acceptor groups. Here we report the photophysical and electronic properties of the trans to cis isomerization of 1-(pyridin-4-yl)-2-(N-methylpyrrol-2-yl)ethene ligand (mepepy) in aqueous solution using photoacoustic calorimetry (PAC) and theoretical methods. Density functional theory (DFT) calculations demonstrate a global energy difference between cis and trans isomers of mepepy to be 8 kcal mol(-1), while a slightly lower energy is observed between the local minima for the trans and cis isomers (7 kcal mol(-1)). Interestingly, the trans isomer appears to exhibit two ground-state minima separated by an energy barrier of approximately 9 kcal mol(-1). Results from the PAC studies indicate that the trans to cis isomerization results in a negligible volume change (0.9 +/- 0.4 mL mol(-1)) and an enthalpy change of 18 +/- 3 kcal mol(-1). The fact that the acoustic waves associated with the trans to cis transition of mepepy overlap in frequency with those of a calorimetric reference implies that the conformational transition occurs faster than the approximately 50 ns response time of the acoustic detector. Comparison of the experimental results with theoretical studies provide evidence for a mechanism in which the trans to cis isomerization of mepepy results in the loss of a hydrogen bond between a water molecule and the pyridine ring of mepepy.

Resonance enhanced multiphoton ionization spectroscopy and theoretical calculations of cis and trans p-methoxystyrene rotamers

The structures and vibrations of p-methoxystyrene in the first electronically excited state (S 1) were studied by mass analyzed resonance-enhanced two photon ionization (R2PI) spectroscopy and theoretical calculations. The ab initio and the density functional theory (DFT) calculations reveal that two rotamers, cis and trans, are stable in both the ground S 0 state and the excited S 1 state, and their optimized molecular geometries are achieved. The band origins of the S 1 ← S 0 electronic transition of cis and trans p-methoxystyrene are measured to be 33242 and 33324 cm −1, respectively. Assignment of the observed spectral bands of the two rotamers in the excited S 1 state was made mainly based on the ab initio calculations and the conformity with the available data in the literature.