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This work shows how the N 1s photoemission (PE) spectrum of self-associated melamine molecules in aqueous solution has been successfully rationalized using an integrated computational approach encompassing classical metadynamics simulations and quantum calculations based on density functional theory (DFT). The first approach allowed us to describe interacting melamine molecules in explicit waters and to identify dimeric configurations based on π–π and/or H-bonding interactions. Then, N 1s binding energies (BEs) and PE spectra were computed at the DFT level for all structures both in the gas phase and in an implicit solvent. While pure π-stacked dimers show gas-phase PE spectra almost identical to that of the monomer, those of the H-bonded dimers are sensibly affected by NH···NH or NH···NC interactions. Interestingly, the solvation suppresses all of the non-equivalences due to the H-bonds yielding similar PE spectra for all dimers, matching very well our measurements.

Challenging the basis of our chemical intuition, recent experimental evidence reveals the presence of a new type of intrinsic fluorescence in biomolecules that exists even in the absence of aromatic or electronically conjugated chemical compounds. The origin of this phenomenon has remained elusive so far. In the present study, we identify a mechanism underlying this new type of fluorescence in different biological aggregates. By employing non-adiabatic ab initio molecular dynamics simulations combined with an unsupervised learning approach, we characterize the typical ultrafast non-radiative relaxation pathways active in non-fluorescent peptides. We show that the key vibrational mode for the non-radiative decay towards the ground state is the carbonyl elongation. Non-aromatic fluorescence appears to emerge from blocking this mode with strong local interactions such as hydrogen bonds. This "carbonyl-lock" mechanism for trapping the excited state leads to the fluorescence yield increase observed experimentally, and paves the way for design principles to realize novel non-invasive biocompatible probes with applications in bioimaging, sensing, and biophotonics.

Amyloids have unique structural, chemical, and optical properties. Although much theoretical effort has been directed toward understanding amyloid nucleation, the understanding of their optical properties has remained rather limited. In particular, the photophysical mechanisms leading to near-UV excitation and characteristic blue-green luminescence in amyloid systems devoid of aromatic amino acids have not been resolved. We use ab initio static calculations and nonadiabatic dynamics simulations to study the excited electronic states of model amyloid-like peptides. We show that their photophysics is essentially governed by the multitude of nπ* states with excitation localized on the amide groups. The strong stabilization of the nπ* states with respect to the amide group deplanarization and the concomitant increase of the oscillator strength make excitation in the near-UV possible. With respect to emission, our dynamics simulations revealed that the amyloid cross β arrangement effectively hinders the nonradiative relaxation channels usually operative in proteins. Finally, we show that after relaxation of the photoexcited peptides toward the minimum of the different nπ* states, fluorescence takes place in the visible (green) part of the electromagnetic spectrum.

Photoelectron angular distribution (PAD) in the laboratory frame for randomly oriented molecules is typically described by a single anisotropy parameter, the so-called asymmetry parameter. However, especially from a theoretical perspective, it is more natural to consider molecular photoionization by using a molecular frame. The molecular frame PADs (MFPADs) may be used to extract information about the electronic structure of the system studied. In the last decade, significant experimental efforts have been directed to MFPAD measurements. MFPADs are highly characterizing signatures of the final ionic states. In particular, they are very sensitive to the nature of the final state, which is embodied in the corresponding Dyson orbital. In our previous work on acetylacetone, a prototype system for studying intra-molecular hydrogen bond interactions, we followed the dynamics of the excited states involved in the photoexcitation–deexcitation process of this molecule. It remains to be explored the possibility of discriminating between different excited states through the MFPAD profiles. The calculation of MFPADs to differentiate excited states can pave the way to the possibility of a clear discrimination for all the cases where the recognition of excited states is otherwise intricate.

Recently, so-called "nontraditional intrinsic luminescence" has been reported in several macromolecular systems. Although DABCO (1,4-diazabicyclo[2.2.2]octane) is the first system in which the effect was observed, a thorough analysis of the optical properties of the molecule, which would reveal the origin of this mysterious effect, is still pending. We perform an advanced post-Hartree-Fock treatment of the low-lying electronic states of this molecule, which need to be described with care because of their pronounced Rydberg character. We take a deeper look into the low-lying electronic transitions of DABCO targeting the explanation of the complex vibronic structures of its absorption and fluorescence spectra. Two electronic states, the

UV irradiation of RNA leads to the formation of intra- and inter-strand crosslinks of cyclobutane type. Despite the importance of this reaction, relatively little is known about how the mutual orientation of the two bases affects the outcome of the reaction. Here we report a comparative nonadiabatic molecular dynamics study of face-to-back (F2B) and face-to-face (F2F) stacked uracil-water clusters. The computations were performed using the second-order algebraic-diagrammatic-construction (ADC(2)) method. We found that F2B stacked uracil-water clusters either relax non-reactively to the ground state by an ethylenic twist around the CC bond or remain in the lowest nπ* state in which the two bases gradually move away from each other. This finding is consistent with the low propensity for the formation of intra-strand cyclobutane dimers between adjacent RNA bases. On the contrary, in F2F stacked uracil-water clusters, in addition to non-reactive deactivation, we found a pro-reactive deactivation pathway, which may lead to the formation of cyclobutane uracil dimers in the electronic ground state. On a qualitative level, the observed photodynamics of F2F stacked uracil-water clusters explains the greater propensity of RNA to form inter-strand cyclobutane-type crosslinks.

Two-dimensional (2D) electronic spectroscopy is a powerful nonlinear technique which provides spectroscopic information on two frequency axes as well as dynamical information as a function of the so-called waiting time. Herein, an ab initio theoretical framework for the simulation of electronic 2D spectra has been developed. The method is based on the classical approximation to the doorway-window representation of three-pulse photon-echo signals and the description of nuclear motion by classical trajectories. Nonadiabatic effects are taken into account by a trajectory surface-hopping algorithm. 2D electronic spectra were simulated with ab initio on-the-fly trajectory calculations using the ADC(2) electronic-structure method for the pyrazine molecule, which is a benchmark system for ultrafast radiationless decay through conical intersections. It is demonstrated that 2D spectroscopy with subfemtosecond UV pulses can provide unprecedented detailed information on the ultrafast photodynamics of polyatomic molecules.

A computational protocol for simulating time-resolved photoelectron signals of medium-sized molecules is presented. The procedure is based on a trajectory surface-hopping description of the excited-state dynamics and a combined Dyson orbital and multicenter B-spline approach for the computation of cross sections and asymmetry parameters. The accuracy of the procedure has been illustrated for the case of ultrafast internal conversion of gas-phase pyrazine excited to the 1B2u(ππ*) state. The simulated spectra and the asymmetry map are compared to the experimental data, and a very good agreement was obtained without applying any energy-dependent rescaling or broadening. An interesting side result of this work is the finding that the signature of the 1Au(nπ*) state is indistinguishable from that of the 1B3u(nπ*) state in the time-resolved photoelectron spectrum. By locating four symmetrically equivalent minima on the lowest-excited (S1) adiabatic potential energy surface of pyrazine, we revealed the strong vibronic coupling of the 1Au(nπ*) and 1B3u(nπ*) states near the S1 ← S0 band origin.

Despite many studies, the mechanisms of nonradiative relaxation of uracil in the gas phase and in aqueous solution are still not fully resolved. Here we combine theoretical UV absorption spectroscopy with nonadiabatic dynamics simulations to identify the photophysical mechanisms that can give rise to experimentally observed decay time constants. We first compute and theoretically assign the electronic spectra of uracil using the second-order algebraic-diagrammatic-construction (ADC(2)) method. The obtained electronic states, their energy differences and state-specific solvation effects are the prerequisites for understanding the photodynamics. We then use nonadiabatic trajectory-surface-hopping dynamics simulations to investigate the photoinduced dynamics of uracil and uracil-water clusters. In contrast to previous studies, we found that a single mechanism - the ethylenic twist around the C[double bond, length as m-dash]C bond - is responsible for the ultrafast component of the nonradiative decay, both in the gas phase and in solution. Very good agreement with the experimentally determined ultrashort decay time constants is obtained.

Although diazoalkanes are important carbene precursors in organic synthesis, a comprehensive mechanism of photochemi-cal formation of carbenes from diazoalkanes has not been proposed. Synergy of experiments and computations demon-strates the involvement of higher excited singlet states in the photochemistry of diazoalkanes. In all investigated diazo-alkanes, excitation to S1 results in nonreactive internal conversion to S0. On the contrary, excitation to higher-lying singlet states (Sn, n > 1), drives the reaction toward a different segment of the S1/S0 conical intersection seam and results in nitrogen elimination and formation of carbenes.

Does the optically bright $$B_2(\pi \rightarrow \pi ^*)$$ transition in pyrrole correspond to an inter-valence or to a mixed valence–Rydberg transition? State-of-the-art electronic structure methods provide inconclusive results and relegate the answer to future time-resolved photoelectron spectroscopy experiments. Here, benchmark calculations of photoionization cross sections, asymmetry parameters and molecular frame photoelectron angular distributions (MFPADs) have been performed with the aim of discerning between the two types of transitions. In particular, we show that MFPADs are very sensitive probes of the electronic wave function and that accurate experimental MFPADs could be used to identify the electronic character of the $$B_2$$ state.

In this computational study we explore the photodynamics of malonaldehyde and compare it to that of the homologous acetylacetone. Upon photoexcitation to the bright S 2 ( π π ∗ ) state malonaldehyde relaxes to the S 1 ( n π ∗ ) state on an ultrashort time scale. Once in the S 1 ( n π ∗ ) state the population of malonaldehyde splits. Part of the population undergoes internal conversion to the ground state by deplanarization of the H-chelate ring, while the other part crosses to the triplet manifold. The comparison with acetylacetone reveals a substantial increase of the internal conversion pathways, from less than 20% in acetylacetone to 40% in malonaldehyde. We show that the substitution of the aliphatic hydrogens by the methyl groups reduces the accessibility of the S1/S0 conical intersection seam in acetylacetone. The system then crosses to the triplet manifold and homolytic C–CH3 bond cleavage takes place.

The photoisomerization of the all-trans protonated Schiff base of retinal (SBR+) in solution is highly inefficient. The present theoretical and experimental investigation aims at disclosing the mechanisms of ultrafast, non-reactive relaxation of SBR+ that lead to the drastic decrease in the isomerization yield in non- polar solvents. Our pump–probe measurements demonstrate the sensitivity of the all-trans SBR+ excited-state dynamics on the electrostatic interaction with the surrounding counterions and the crucial importance of the chromophore microenvironment. Our computational study focuses for the first time on the retinal chromophore–counterion pairs that are formed in non-polar solvents. By employing TDDFT-based nonadiabatic dynamics simulations and ADC(2) reaction paths calculations we found that internal conversion from the initially excited state to an inter- molecular charge transfer state with excitation localized on the counterion, leads to dissociation of the chromophore–counterion pair and to the abortion of isomerization. Barriers to conical intersection with the inter-molecular charge transfer state were found in the range 0.42–0.67 eV at the ADC(2) level. The existence of a barrier along the non-reactive relaxation pathways explains the observation that in solution the excitation on the blue edge of the SBR+ absorption leads to decrease in the isomerization yield with respect to the excitation at the red edge.

The present work is directed toward understanding the mechanisms of excited state deactivation in three neutral model peptides containing the phenylalanine residue. The excited state dynamics of the γL(g+) folded form of N-acetylphenylalaninylamide (NAPA B) and its amide-N-methylated derivative (NAPMA B) is reviewed and compared to the dynamics of the monohydrated structure of NAPA (NAPAH). The goal is to unravel how the environment, and in particular solvation, impacts the photodynamics of peptides. The systems are investigated using reaction path calculations and surface hopping nonadiabatic dynamics based on the coupled cluster doubles (CC2) method and time-dependent density functional theory. The work emphasizes the role that excitation transfer from the phenyl ππ* to amide nπ* state plays in the deactivation of the three systems and shows how the ease of out-of-plane distortions of the amide group determines the rate of population transfer between the two electronic states. The subsequent dynamics on the nπ* state is barrierless along several pathways and leads to fast deactivation to the ground electronic state.

The computational analysis of the isomer- and conformer-dependent photochemistry of 1- and 2-naphthols and their microsolvated water clusters is motivated by their very different excited state reactivities. We present evidence that 1- and 2-naphthol follow distinct excited state deactivation pathways. The deactivation of 2-naphthols, 2-naphthol water clusters, as well as of the anti conformer of 1-naphthol is mediated by the optically dark

The computational analysis of the isomer-and conformer-dependent photochemistry of 1- and 2- naphthols and their microsolvated water clusters is motivated by their very different excited state reactivities. We present evidence that 1- and 2- naphthol follow distinct excited state deactivation pathways. The deactivation of 2- naphthols, 2-naphthol water clusters, as well as of the anti conformer of 1-naphthol is mediated by the optically dark (1)pi sigma* state. The dynamics of the (1)pi sigma* surface leads to the homolytic cleavage of the OH bond. On the contrary, the excited state deactivation of syn 1- naphthol and 1-naphthol water clusters follows an uncommon reaction pathway. Upon excitation to the bright (1)pi pi*(L-a) state, a highly specific excited state hydrogen transfer (ESHT) to carbon atoms C8 and C5 takes place, yielding 1, 8- and 1, 5-naphthoquinone methides. The ESHT pathway arises from the intrinsic electronic properties of the (1)pi pi*(L-a) state of 1-naphthols.

Kynurenines are UV filters found in the human ocular lens which protect the retina from radiation damage. We report on ab initio investigations of the photochemistry of the cis and trans conformers of kynurenine and of an intramolecularly hydrogen-bonded conformer of 3-hydroxykynurenine O-β-d-glucoside. We have explored the excited-state reaction paths for several radiationless excited-state deactivation processes in kynurenines. We show that electron-driven proton-transfer processes mediated by an excited state of charge-transfer character exhibit negligible barriers and that the relevant potential-energy profiles are lower in energy than the lowest absorbing ππ* state. In these proton-transfer processes, a proton moves from one of the amino groups of kynurenine to the keto group. We also report on nonadiabatic trajectory-surface-hopping molecular-dynamics simulations for photoexcited kynurenine. These simulations show that the cis and trans conformers of kynurenine deactivate on a femtosecond-to-picosecond time scale preferably via electron-driven proton transfer from one of the amino groups to the keto group. Cis kynurenine deactivates via a ring-N—H···O═C proton-transfer process. Trans kynurenine tends to undergo trans → cis isomerization before deactivating via the same process. These results suggest that the deactivation process involving the ring-amino group in the cis conformer of kynurenine is the most efficient excited-state deactivation process in kynurenines. The joint electronic-structure calculations and dynamics simulations provide a new level of mechanistic insight into the efficient UV-filtering capacity of kynurenines.

Hydroxylamine is a prototypical molecule displaying OH and NH bond interactions. Despite the early interest in the photolysis of NH 2 OH the primary mechanism of photodissociation remained unclear. Here we perform nonadiabatic trajectory-surface-hopping dynamics simulations based on the algebraic diagrammatic construction method to the second order (ADC(2)) together with reaction path calculations based on the multi-state complete active space second-order perturbation theory (CASPT2) method to identify the dominant deactivation channel of NH 2 OH. By considering the photoinduced dynamics of hydroxylamine hydrates, ranging from monohydrates to tetrahydrates we show how this channel is modified by site-specific addition of water.

The potential energy surface of the formic acid dimer is investigated in the vicinity of the minima. The linear absorption IR spectrum in the region of the O–H antisymmetric stretch is analyzed using a combination of a second-order perturbative treatment and non-perturbative calculations in reduced dimensionality. The importance of particular coupling mechanisms is studied systematically and it has been shown that the red-shift of the ν OH ( B u ) center frequency is almost exclusively caused by the Davydov coupling to the symmetric O–H stretching vibration. We find that anharmonic couplings to low frequency dimer stretching and rocking modes, and Fermi resonances to mid-infrared modes contribute to the width, but only in a minor extent to the frequency of the ν OH ( B u ) band maximum.

The excitation wavelength dependent photodynamics of pyrrole are investigated by nonadiabatic trajectory-surface-hopping dynamics simulations based on time dependent density functional theory (TDDFT) and the algebraic diagrammatic construction method to the second order (ADC(2)). The ADC(2) results confirm that the N-H bond dissociation occurring upon excitation at the origin of the first excited state, S-1(pi sigma*), is driven by tunnelling [Roberts et al., Faraday Discuss., 2013, 163, 95] as a barrier of DE = 1780 cm(-1) traps the population in a quasi-bound minimum. Upon excitation to S-1(pi sigma*) in the wavelength range of 236-240 nm, direct dissociation of the N-H bond takes place with a time constant of 28 fs. The computed time constant is in very good agreement with recently reported measurements. Excitation to the lowest B-2 state in the 198-202 nm range returns a time constant for N-H fission of 48 fs at the B3LYP/def2-TZVPD level, in perfect agreement with the experiment [Roberts et al. Faraday Discuss., 2013, 163, 95]. For the same wavelength range the ADC(2)/aug-cc-pVDZ decay constant is more than three times longer than the experimentally reported one. The accuracy of the B3LYP/def2-TZVPD dynamics is checked against reference complete-active-space second-order perturbation theory (CASPT2) calculations and explained in terms of correct topography of the pi pi* surface and the lack of mixing between the pi pi* and the 3p(x) Rydberg states which occurs in the ADC(2) method.

The intramolecular hydrogen bond in the enol-acethylacetone (ACAC) is investigated by performing reduced-dimensional quantum calculations. To analyze the shared proton vibrations, two sets of coordinates were employed: normal mode coordinates describing the motion in the vicinity of the most stable configuration, and internal coordinates accounting for the double minimum proton motion. It is proved that the extreme broadness of the OH-stretch band in ACAC is a consequence of the coexistence of two enol-ACAC structures: the global minimum and the transition state for rotation of the distal methyl group. Further, a ground-state tunneling splitting of 116 cm(-1) is found, and it is shown that the inclusion of the kinematic coupling is mandatory when treating large-amplitude proton motion. In the OH-stretch direction a splitting of 853 cm(-1) was predicted.

Proton tunneling in malonaldehyde (MA) is investigated. Three-dimensional potential energy surfaces spanned by the O⋯H⋯O fragment of MA were generated based on DFT and reparameterized semiempirical calculations. The energy splitting of 42.3 (15.3) and 24.3 (5.3) cm −1 at the DFT and semiempirical levels, respectively, find good agreement with the experimental values. The splitting is reduced to 36.4 (12.5) cm −1 and to 18.6 (2.9) cm −1 by introducing an effective mass for the heavy atoms. We show that the potential barrier of 4.0 kcal mol −1 is consistent with the observed H (D) tunneling splitting of 21.6 (2.9) cm −1 .

International audience; A conformation-selective photophysics study in phenylalanine model peptides, combining pump-probe gas phase experiments and excited state calculations, highlights for the first time the quenching properties of a primary amide group (through its nπ* excited state) along with the effect of vibrational energy that facilitates access to the conical intersection area.

Aminophenyl-substituted adamantane-dipyrromethane receptors 1 and 2 and aminophenylpyrrole 3 showed a very pronounced and unique UV spectral response with in aprotic as well as in aqueous media. The fitting of the binding isotherms with indicated formation of the complexes with the 1:2 (host–anion) stoichiometry. ESI-MS study with mixtures of receptor 3 and tetrabutylammonium hydrogensulfate of different ratios indicated an association of the and receptor 3, as well as association of the species into dimers. The unique UV spectral response with is proposed to be due to proton transfer from to the amino group of the receptor, which in an aprotic solvent probably takes place in the corresponding H-bonded complexes. The assignations of the spectral changes were corroborated by computation. Moreover, theoretical study indicated that ‘intra-supramolecular’ proton transfer took place, whereas the presence of the second was required to enhance the acidity of the first H-bonded anion.

Different schemes for controlling the isomerization of thioacetylacetone by means of shaped laser pulses are investigated here. A two--dimensional analytical model potential function is proposed which captures the essential features of the transfer process, i.e. the H--atom motion and the heavy atom rearrangement. The parameters for this model potential are derived from high level ab initio quantum chemical calculations. The influence of those degrees of freedom which are not treated explicitly is modeled by means of their spectral density within density matrix theory. Various laser control strategies are studied putting emphasis on their robustness with respect to relaxation and dephasing processes. Laser pulse shapes are derived from the coherent dynamics by adjusting the parameters of analytically given fields and by using optimal control theory. It is found that compared to pump--dump control, laser driven hydrogen tunneling is more suited to achieve high yields in condensed phase situations. The applicability to other molecular systems showing intramolecular hydrogen transfer is discussed.

Isomerization reactions from a reactant state to a near-degenerate product state which are typical for intramolecular hydrogen transfer may be achieved by means of ultrashort picosecond or sub-picosecond laser pulses having three consecutive time domains: Initially, the laser field is switched on such that the wave packet representing the reactant is converted into a superposition of near-degenerate delocalized states of the "dressed" molecule In the second stage, the laser field is kept approximately constant until the wave packet has tunneled from the reactant to the product configuration, during the tunneling time. Finally the field is switched off such that the wave packet is stabilized as the target product state. This approach is suggested by optimal control theory and applied to a one--dimensional model resembling substituted malonaldehydes. Here it is found that the laser driven tunneling requires time--integrated laser field intensities fifty times smaller than the alternative pump--dump approach which drives the reactant wave packet over the potential barrier towards the product state without tunneling. Various applications and extensions of this method are discussed.

ESIPT and solvent-assisted ESPT in isomeric phenyl naphthols and naphthyl phenols 5-8 were investigated by preparative photolyses in CH3CN-D2O, fluorescence spectroscopy, LFP, and ab initio calculations. ESIPT takes place only in 5 (D-exchange Φ = 0.3), whereas 6-8 undergo solvent-assisted PT with much lower efficiencies. The efficiency of the ESIPT and solvent-assisted PT is mainly determined by different populations of the reactive conformers in the ground state and the NEER principle. The D-exchange experiments and calculations using RI-CC2/cc-pVDZ show that 5 in S1 deactivate by direct ESIPT from the OH to the naphthalene position 1 through a conical intersection with S0, delivering QM 14 that was detected by LFP (τ = 26 ± 3 ns). ESIPT to the position 3 in 5 is possible but it proceeds from a less-populated conformer and involves an energy barrier on S1. In solvent-assisted PT to the naphthalene position 4 in 5, zwitterion 17 is formed that cyclizes to stable naphthofuran photoproducts 9-12. The regiochemistry of the deuteration in solvent-assisted PT was correlated with the NBO charges of the corresponding phenolates/naphtholates 5- - 8-. Combined experimental and theoretical data indicate that solvent-assisted PT takes place via a sequential mechanism involving first deprotonation of the phenol/naphthol, followed by the protonation by H2O in the S1 state of phenolate/naphtholate. The site of protonation by H2O is mostly at the naphthalene α-position.

Dynamics of a particle in the plane electromagnetic wave is investigated by classical theory. By introducing the uncertainty principle into classical theory it is possible to explain the frequency dependent energy transfer in this interaction. Comparison with quantum theory is made and a very good agreement is found in almost all cases. Classical theory fails to describe a resonant process which occurs at a particular frequency of the electromagnetic plane wave.

International audience; The mechanisms of nonradiative deactivation of a phenylalanine residue after near-UV photoexcitation have been investigated in an isolated peptide chain model (N-acetylphenylalaninylamide, NAPA) both experimentally and theoretically. Lifetime measurements at the origin of the first ππ* state of jet-cooled NAPA molecules have shown that (i) among the three most stable conformers of the molecule, the folded conformer NAPA B is ∼50-times shorter lived than the extended major conformer NAPA A and (ii) this lifetime is virtually insensitive to deuteration at the NH(2) and NH sites. Concurrent time-dependent density functional theory (TDDFT) based nonadiabatic dynamics simulations in the full dimensionality, carried out for the NAPA B conformer, provided direct insights on novel classes of ultrafast deactivation mechanisms, proceeding through several conical intersections and leading in fine to the ground state. These mechanisms are found to be triggered either (i) by a stretch of the N(Phe)H bond, which leads to an H-transfer to the ring, or (ii) by specific backbone amide distortions. The potential energy surfaces of the NAPA conformers along these critical pathways have been characterized more accurately using the coupled cluster doubles (CC2) method and shown to exhibit barriers that can be overcome with moderate excess energies. These results analyzed in the light of the experimental findings enabled us to assign the short lifetime of NAPA B conformer to a number of easily accessible exit channels from the initial ππ* surface, most importantly the one involving a transfer of electronic excitation to an nπ* surface, induced by distortions of the backbone peptide bond.

Irradiation of 2-phenyl-1- naphthol (6 )i n CH 3CN/D2O (3:1) leads to very efficient incorporation of deuterium at the ortho-positions of the adjacent phenyl ring (overall F = 0.73 0.07), along with minor incorpo- ration at the naphthalene positions 5 and 8. These finding are explained by excited state intramolecular proton transfer (ESIPT) from the phenolic OH group to the corresponding carbon atoms, the main pathway giving rise to quinone methide (QM) 7, which has been characterized by LFP (t 20 ns; 460 nm). The ESIPT reaction paths have been explored with the second order approximate coupled cluster (CC2) method. In nonprotic solvents the ESIPT from the naphthol O-H to the ortho-position of the phenyl ring proceeds in a barrierless manner along the 1 La energy surface via a conical in- tersection with the S0 state, delivering 7. In aqueous solvent, clusters with H2O are formed wherein proton trans- fer (PT) to solvent and a H2O-mediat- ed relay mechanism gives rise to naph- tholates and QMs. The results are com- pared with 2-phenylphenol (3) that also undergoes barrierless ESIPT giving a QM via a conical intersection. However, due to an unfavorable con- formation in the ground state, the quantum efficiency for ESIPT of 3 is significantly lower (F for D-ex- change = 0.041). These results show that ESIPT from phenol to carbon need not be an intrinsically inefficient process.

Nonadiabatic dynamics in the framework of time-dependent density functional theory was used to simulate gas-phase relaxation dynamics of pairs of conformations of formic acid monomers (cis and trans FAM) and dimers (acyclic aFAD and cyclic cFAD). In the early phase of the excited state dynamics, elongation of the C═O bond and pyramidalization of the carbon atom is observed in both FAM and FAD. Subsequently, the photodynamics of FAM is shown to be dominated by fragmentation processes occurring mostly in the excited state and resulting in HCO and OH radicals. In only a few cases does the dissociation take place from the vibrationally excited ground electronic state, whereby CO and H(2)O are the major reaction products. In the dimers, single proton transfer triggers ultrafast relaxation to the ground electronic state. In the single hydrogen bonded dimer about half of the trajectories dissociate into electronically excited monomers, whereas this potentially destructive dissociation is effectively suppressed in the double hydrogen bonded dimer. Upon relaxation to the ground electronic state, separation of FAD into monomers takes place, but without their further fragmentation on the time scale of the simulation. We conclude that the crucial difference between the FAM and FAD photodynamics is that the latter is dominated by nondestructive radiationless deactivation pathways during which a key protective role is assumed by the single (aFAD) or double (cFAD) intermonomer hydrogen bonds.

The vibrational spectra of the protonated Schiff base of n-butylretinal (nSBR+) in dichloromethane are studied. The trifluoroacetic acid (TFA) is used for the protonation of the Schiff base of nbutylretinal (nSBR). Combining the two-dimensional correlation analysis of the experimental infrared spectra with anharmonic frequency calculations it is shown that two types of ionic aggregates between nSBR+ and the TFA counterion are formed. The study suggests that the interaction between nSBR+ and the TFA counterion may be responsible for the observed lost of photoselectivity in the trans-cis isomerization of the nSBR+ in solution. (doi: 10.5562/cca1826)

An extensive computational study of the conformational preferences of three capped dipeptides: Ac-Xxx-Phe-NH(2), Xxx = Gly, Ala, Val is reported. On the basis of local second-order Møller-Plesset perturbation theory (LMP2) and DFT computations we were able to identify the experimentally observed conformers as gamma(L)-gamma(L)(g-) and beta-turn I(g+) in Ac-Gly-Phe-NH(2), and Ac-Ala-Phe-NH(2), and as the closely related gamma(L)(g+)-gamma(L)(g-) and beta-turn I(a,g+) in Ac-Val-Phe-NH(2). In contrast to the experimental observation that peptides with bulky side chain have a propensity for beta-turns, we show that in Ac-Val-Phe-NH(2) the minimum energy structure corresponds to the experimentally non detected beta-strand.

Combining two-color infared pump-probe spectroscopy and anharmonic force field calculations we characterize the anharmonic coupling patterns between fingerprint modes and the hydrogen-bonded symmetric vNH2 stretching vibration in adenine-thymine dA20-dT20 DNA oligomers. Specifically, it is shown that the anharmonic coupling between the δNH2 bending and the vC4=O4 stretching vibration, both absorbing around 1665 cm-1, can be used to assign the vNH2 fundamental transition at 3215 cm-1 despite the broad background absorption of water.

The potential energy surface of the acetic acid dimer relevant to the intermolecular hydrogen bond dynamics is studied. Apart fr the minimum energy structure exhibiting C 2h symmetry the H-transfer dynamics is strongly influenced by two rotamer structures obtained by a 60° internal rotation of one or both methyl groups. It was found that the characteristic multi-band structure of the OH-stretching range is caused by the coexistence of these three conformers. It is also shown that the large frequency shift of the OH stretch bands with respect to the harmonic values, arises from the anharmonicity of the two local OH-stretch modes.

We consider the effect of isotopic labeling on the electric charge distribution and dynamics of the formic acid dimer. Our investigation is based on accurate ab initio calculations of vibrationally induced dipole moments and multidimensional quantum calculations of vibrational ground-state splittings. It is found that non-negligible dipole moments of μ = 0.032 D and μ = 0.021 D arise in HCOOH− DOOCD and HCOOH− DOOCH, respectively, suggesting the feasibility of microwave studies. Within the reaction surface Hamiltonian approach a ratio of splittings of 1:0.2:0.045 is predicted for HCOOH− HOOCH:HCOOH− DOOCH:HCOOD− DOOCH.

We investigate the control of state-selective population transfer in the THz spectral range generated by sub-one-cycle pulse excitation. To this end we developed a zero-net-force modification of the optimal control algorithm which allows us to extend the algorithm into the ultrashort pulse domain. By combining the analysis of the control landscapes and that of optimal control theory, we were able to formulate a general mechanism suitable for laser control by ultrashort pulses. The strategy consists of a superposition of two $\pi$-pulses with carrier envelope phases of $\phi = \pi/2$. The first pulse is effectively in resonance with the targeted transition, while the second one, fired at around the minimum of the first pulse second lobe removes leaking to the dipole-coupled background state. In order to compensate for the pulses ultrashort duration, the carrier frequencies of both pulses are red-shifted from the spectroscopic resonance.

State selective preparation and manipulation of discrete-level quantum systems such as atoms, molecules or quantum dots is a the ultimate tool for many diverse fields such as laser control of chemical reactions, atom optics, high-precision metrology and quantum computing. Rabi oscillations are one of the simplest, yet potentially quite useful mechanisms for achieving such manipulation. Rabi theory establishes that in the two-level systems resonant drive leads to the periodic and complete population oscillations between the two system levels. In this paper an analytic optimization algorithm for producing Rabi-like oscillations in the general discrete many-level quantum systems is presented., Published in Phys.Rev.A. This is the final published version

An index measuring the mathematical content of an interdisciplinary area is described and calculated for the MATH/CHEM/COMP conference. Some further areas of application of this index in mathematical chemistry are indicated.

This paper investigates the effect of Redfield relaxation on the control of state selective excitation in a two-dimensional model system. The model potential, tailored to DFT data for picolinic acid N-oxide, comprises the proton transfer and the heavy atom coordinate. The present study shows that selective excitation of the O-H stretching mode can be achieved by simple analytical pulses satisfying the pi pulse condition. The efficiency of the preparation is tested against the instability of pulse characteristics.

Laser control of a hydrogen transfer reaction in a small model system embedded in a condensed phase environment is investigated. The two-dimensional model comprises those features of the multi-dimensional potential energy surface of thioacetylacetone which are most relevant for the isomerization reaction from the enol to the enethiol configuration. The influence of the remaining intramolecular coordinates as well as of a possible environment is described by a spectral density within the reduced density matrix approach. Different forms of the driving infrared laser pulse are explored placing emphasis on their capability for competing successfully with relaxation processes. The reaction dynamics is characterized by calculating the nonlinear optical response nonperturbatively in the driving field.

Herbicides are chemical molecules used for destruction of weeds. Massive usage of herbicides has resulted in two global problems: increase in weed resistance and harmful impact of human health [1, 2]. In order to facilitate development of novel, more specific herbicides and of strategies for impeding the weed resistance, we have carried out extensive in silico analysis of the set of herbicides. Herein, we present results revealing links between structural, physicochemical, ADME (Absorption, Distribution, Metabolism, Excretion) and toxic features for herbicides (Figure 1). The analysis has been done by using proper machine learning approaches. References: [1] A. Forouzesh, E. Zand, S. Soufizadeh, S. S. Foroushani, Weed Res. 55 (2015) 334-358. [2] V. I. Lushchak, T. M. Matviishyn, V. V. Husak, J. M. Storey, K. B. Storey, EXCLI J. 17 (2018) 1101-1136.

Aminoacyl-tRNA synthetases (aaRS) catalyze formation of the cognate pair between amino acid and tRNA via ATP-dependent two-step reaction. Firstly amino acid is activated to yield an aminoacyl-adenylate (aa-AMP) intermediate followed by the transfer of amino acid to tRNA. The accuracy of this reaction is essential for the fidelity of protein biosynthesis since attached amino acid is not additionally proofread during the selection of aminoacylated tRNAs at the ribosome. While aaRSs are able to recognize cognate tRNA substrate with high accuracy due to large contact surface area, accurate selection of cognate amino acid from near-cognate ones could be critical because of smaller contact area and similar chemical structures of their side chains. As a result, some aaRSs proceed in misactivation of noncognate amino acid and its subsequent transfer to tRNA. In order to keep pace with the tolerable error in protein biosynthesis, aaRSs have evolved hydrolytic editing or proofreading to correct these errors. It is well established that correction of misacylated tRNA (post-transfer editing) occurs in a second, spatially separated, active site located at the editing domain. However, the exact place, mechanism and role for tRNA in pre-transfer editing (hydrolysis of noncognate aa-AMP) are still not understood in detail and several new lines of evidence [1] question the model previously proposed [2]. Here we show that both isoleucyl and valyl-tRNA-synthetases (IleRS and ValRS, respectively) possess tRNA-independent pre-transfer editing comprising 5% of overall proofreading activity. Addition of tRNA highly stimulates proofreading but the mechanism is not completely understood yet. Our findings contradict the broadly accepted model [2] which assumes that tRNA is indispensable for noncognate aa-AMP hydrolysis. Several IleRS and ValRS mutants, bearing mutations in the distant editing site, were cloned and purified. Steady-state and pre-steady state analyses are performed at the moment to clarify whether this activity occurs within the confines of the synthetic site and to elucidate the mechanism of hydrolysis in the absence of tRNA. In order to prepare huge amount of tRNA for kinetic analysis of tRNA-dependent proofreading, tRNAIle and tRNAVal major isoacceptor genes were cloned and overexpressed in vivo. Up to now, tRNAIle isoacceptor has been isolated by reverse-phase chromatography. [1] S.S. Yadavalli, K. Musier-Forsyth and M. Ibba, Proc. Natl. Acad. Sci. USA, 105 (2008) 19031 [2] A.C. Bishop, T.K. Nomanbhoy and P. Schimmel, Proc. Natl. Acad. Sci. USA, 99, (2002) 585

The therapeutic index (TI) of peptide antibiotics is defined as the ratio of hemolytic to antimicrobial activity. We constructed the database of 51 non-homologous helical antimicrobial peptides, isolated from frogs, with associated therapeutic index values determined on E. coli and human erythrocytes. Sequence attributes calculated by the SPLIT 3.5 server (split.pmfst.hr/split) are used for developing relationships between peptide structure and its therapeutic index. Helical amphipathic segments and G, Q, H, D, E amino acid frequencies are positively correlated with TI. High preferences for transmembrane helix conformation are negatively correlated with TI. The composite predictor is developed as a specific combination of these sequence-based parameters. Corresponding log-log model for estimating the therapeutic index exhibits good correlation (r = 0.9) with experimental TI values.