Proton transfer in nucleobases is mediated by water.

Water plays a central role in chemistry and biology by mediating the interactions between molecules, altering energy levels of solvated species, modifying potential energy profiles along reaction coordinates, and facilitating efficient proton transport through ion channels and interfaces. This study investigates proton transfer in a model system comprising dry and microhydrated clusters of nucleobases. With mass spectrometry and tunable vacuum ultraviolet synchrotron radiation, we show that water shuts down ionization-induced proton transfer between nucleobases, which is very efficient in dry clusters.

[Structure of heterotrophic plankton in the littoral zone of the plain reservoir under effect of hydrophilic birds].

The eutrophic effect of products of vital activity of colonies of hydrophilic birds on the community of heterotrophic plankton in shallow parts of the plain reservoir is shown. The strongest effect of birds is observed in a protected part of the reservoir. Specific changes in some characteristics of zooplankton as distinct from the response to the anthropogenic effect are found.

Triple-Decker Motif for Red-Shifted Fluorescent Protein Mutants.

Among fluorescent proteins (FPs) used as genetically encoded fluorescent tags, the red-emitting FPs are of particular importance as suitable markers for deep tissue imaging. Using electronic structure calculations, we predict a new structural motif for achieving red-shifted absorption and emission in FPs from the GFP family. By introducing four point mutations, we arrive to the structure with the conventional anionic GFP chromophore sandwiched between two tyrosine residues.

On the photodetachment from the green fluorescent protein chromophore.

Motivated by the discrepancies in recent experimental and theoretical studies of photodetachment from isolated model chromophores of the green fluorescent protein (GFP), this study reports calculations of the electron detachment energies and photoelectron spectra of the phenolate and deprotonated p-hydroxybenzylidene-2,3-dimethylimidazolinone (HBDI) anions. The spectra were computed using double-harmonic parallel normal mode approximation. High-level coupled-cluster methods as well as density functional theory were used to compute vertical and adiabatic detachment energies of the phenolate anion serving as a model system representing anionic GFP-like chromophores (HBDI).

Toward organic photohydrides: excited-state behavior of 10-methyl-9-phenyl-9,10-dihydroacridine.

The excited-state hydride release from 10-methyl-9-phenyl-9,10-dihydroacridine (PhAcrH) was investigated using steady-state and time-resolved UV/vis absorption spectroscopy. Upon excitation, PhAcrH is oxidized to the corresponding iminium ion (PhAcr(+)), while the solvent (acetonitrile/water mixture) is reduced (52% of PhAcr(+) and 2.5% of hydrogen is formed).

Complex-scaled equation-of-motion coupled-cluster method with single and double substitutions for autoionizing excited states: theory, implementation, and examples.

Theory and implementation of complex-scaled variant of equation-of-motion coupled-cluster method for excitation energies with single and double substitutions (EOM-EE-CCSD) is presented. The complex-scaling formalism extends the EOM-EE-CCSD model to resonance states, i.e.

Effective fragment potential method in Q-CHEM: a guide for users and developers.

A detailed description of the implementation of the effective fragment potential (EFP) method in the Q-CHEM electronic structure package is presented. The Q-CHEM implementation interfaces EFP with standard quantum mechanical (QM) methods such as Hartree-Fock, density functional theory, perturbation theory, and coupled-cluster methods, as well as with methods for electronically excited and open-shell species, for example, configuration interaction, time-dependent density functional theory, and equation-of-motion coupled-cluster models. In addition to the QM/EFP functionality, a "fragment-only" feature is also available (when the system is described by effective fragments only).

Conical Intersection and Potential Energy Surface Features of a Model Retinal Chromophore: Comparison of EOM-CC and Multireference Methods.

This work investigates the performance of equation-of-motion coupled-cluster (EOM-CC) methods for describing the changes in the potential energy surfaces of the penta-2,4-dieniminium cation, a reduced model of the retinal chromophore of visual pigments, due to dynamical electron correlation effects. The ground-state wave function of this model includes charge-transfer and diradical configurations whose weights vary along different displacements and are rapidly changing at the conical intersection between the ground and the first excited states, making the shape of the potential energy surface sensitive to a balanced description of nondynamical and dynamical correlation. Recently, variational (MRCISD) and perturbative (MRPT2) approaches for including dynamical correlation in CASSCF-based calculations were tested along three representative ground state paths.

[Comparative efficacy of pharmacoinvasive strategy of myocardial reperfusion and primary angioplasty in patients with acute ST elevation myocardial infarction].

In order to assess comparative efficacy of pharmacoinvasive strategy of myocardial reperfusion and primary angioplasty in ST elevation acute myocardial infarction 289 patients were randomized at prehospital stage within first 6 hours of the disease into 2 groups: primary angioplasty (group 1), and prehospital thrombolysis with subsequent rescue or delayed angioplasty depending on efficacy of thrombolysis. We analyzed clinical and anamnestic characteristics of patients, efficacy of reperfusion measures, dimensions of myocardial necrosis, and clinical course of the disease. Pharmacoinvasive myocardial reperfusion with prehospital thrombolysis compared with primary coronary angioplasty decreased time of myocardial ischemia (224.

Thulium-doped mode-locked all-fiber laser based on NALM and carbon nanotube saturable absorber.

We present a thulium-doped fiber laser mode-locked by a carboxymetylcellulose high-optical quality film with dispersed single-walled carbon nanotubes. Laser system based on the nonlinear amplifying loop mirror generates the shortest pulses earlier obtained in SWCNT mode-locked thulium-doped fiber lasers with a duration of 450 fs and 18 mW maximum average power at 1870 nm.

Transform-limited pulse generation in normal cavity dispersion erbium doped single-walled carbon nanotubes mode-locked fiber ring laser.

We demonstrate an erbium doped fiber ring laser mode-locked with a carboxymetylcellulose high-optical quality film with dispersed single-walled carbon nanotubes (SWCNT). The laser with large normal net cavity dispersion generates near bandwidth-limited picosecond inverse modified soliton pulses at 1.56 µm.

Four Bases Score a Run: Ab Initio Calculations Quantify a Cooperative Effect of H-Bonding and π-Stacking on the Ionization Energy of Adenine in the AATT Tetramer.

Benchmark calculations of the lowest ionized state of the (A:T)2 (mixed adenine-thymine) cluster at the geometry taken from the DNA X-ray structure are presented. Vertical ionization energies (IEs) computed by the equation-of-motion coupled-cluster method with single and double substitutions are reported and analyzed. The shift in IE relative to the monomer (A) is -0.

Exploring structural and optical properties of fluorescent proteins by squeezing: modeling high-pressure effects on the mStrawberry and mCherry red fluorescent proteins.

Molecular dynamics calculations of pressure effects on mStrawberry and mCherry fluorescent proteins are reported. The simulations reveal that mStrawberry has much floppier structure at atmospheric pressure, as evidenced by larger backbone fluctuations and the coexistence of two conformers that differ by Ser146 orientation. Consequently, pressure increase has a larger effect on mStrawberry, making its structure more rigid and reducing the population of one of the conformers.

Toward understanding the redox properties of model chromophores from the green fluorescent protein family: an interplay between conjugation, resonance stabilization, and solvent effects.

The redox properties of model chromophores from the green fluorescent protein family are characterized computationally using density functional theory with a long-range corrected functional, the equation-of-motion coupled-cluster method, and implicit solvation models. The analysis of electron-donating abilities of the chromophores reveals an intricate interplay between the size of the chromophore, conjugation, resonance stabilization, presence of heteroatoms, and solvent effects. Our best estimates of the gas-phase vertical/adiabatic detachment energies of the deprotonated (i.

De-perturbative corrections for charge-stabilized double ionization potential equation-of-motion coupled-cluster method.

Charge stabilization improves the numeric performance of double ionization potential equation-of-motion (EOM-DIP) method when using unstable (autoionizing) dianion references. However, the stabilization potential introduces an undesirable perturbation to the target states' energies. Here we introduce and benchmark two approaches for removing the perturbation caused by the stabilization.

Toward Molecular-Level Characterization of Photoinduced Decarboxylation of the Green Fluorescent Protein: Accessibility of the Charge-Transfer States.

Irradiation of the green fluorescent protein (GFP) by intense violet or UV light leads to decarboxylation of the Glu222 side chain in the vicinity of the chromophore (Chro). This phenomenon is utilized in optical highlighters, such as photoactivatable GFP (PA-GFP). Using state-of-the-art quantum chemical calculations, we investigate the feasibility of the mechanism proposed in the experimental studies [van Thor et al.

General formulation of spin-flip time-dependent density functional theory using non-collinear kernels: theory, implementation, and benchmarks.

We report an implementation of the spin-flip (SF) variant of time-dependent density functional theory (TD-DFT) within the Tamm-Dancoff approximation and non-collinear (NC) formalism for local, generalized gradient approximation, hybrid, and range-separated functionals. The performance of different functionals is evaluated by extensive benchmark calculations of energy gaps in a variety of diradicals and open-shell atoms. The benchmark set consists of 41 energy gaps.

First-principle protocol for calculating ionization energies and redox potentials of solvated molecules and ions: theory and application to aqueous phenol and phenolate.

The effect of hydration on the lowest vertical ionization energy (VIE) of phenol and phenolate solvated in bulk water was characterized using the equation-of-motion ionization potential coupled-cluster (EOM-IP-CCSD) and effective fragment potential (EFP) methods (referred to as EOM/EFP) and determined experimentally by valence photoemission measurements using microjets and synchrotron radiation. The computed solvent-induced shifts in VIEs (ΔVIEs) are -0.66 and +5.

Ionization of dimethyluracil dimers leads to facile proton transfer in the absence of hydrogen bonds.

Proton transfer is ubiquitous in chemistry and biology, occurring, for example, in proteins, enzyme reactions and across proton channels and pumps. However, it has always been described in the context of hydrogen-bonding networks ('proton wires') acting as proton conduits. Here, we report efficient intramolecular ionization-induced proton transfer across a 1,3-dimethyluracil dimer, a model π-stacked system with no hydrogen bonds.

Overtone-induced dissociation and isomerization dynamics of the hydroxymethyl radical (CH2OH and CD2OH). I. A theoretical study.

The dissociation of the hydroxymethyl radical, CH(2)OH, and its isotopolog, CD(2)OH, following the excitation of high OH stretch overtones is studied by quasi-classical molecular dynamics calculations using a global potential energy surface (PES) fitted to ab initio calculations. The PES includes CH(2)OH and CH(3)O minima, dissociation products, and all relevant barriers. Its analysis shows that the transition states for OH bond fission and isomerization are both very close in energy to the excited vibrational levels reached in recent experiments and involve significant geometry changes relative to the CH(2)OH equilibrium structure.

Insight into the common mechanism of the chromophore formation in the red fluorescent proteins: the elusive blue intermediate revealed.

Understanding the chromophore maturation process in fluorescent proteins is important for the design of proteins with improved properties. Here, we present the results of electronic structure calculations identifying the nature of a blue intermediate, a key species in the process of the red chromophore formation in DsRed, TagRFP, fluorescent timers, and PAmCherry. The chromophore of the blue intermediate has a structure in which the π-system of the imidazole ring is extended by the acylimine bond, which can be represented by the model N-[(5-hydroxy-1H-imidazole-2yl)methylidene]acetamide (HIMA) compound.

A VUV Photoionization and Ab Initio Determination of the Ionization Energy of a Gas-Phase Sugar (Deoxyribose).

The ionization energy of gas-phase deoxyribose was determined using tunable vacuum ultraviolet synchrotron radiation coupled to an effusive thermal source. Adiabatic and vertical ionization energies of the ground and first four excited states of α-pyranose, the structure that dominates in the gas phase, were calculated using high-level electronic structure methods. An appearance energy of 9.

Effect of microhydration on the electronic structure of the chromophores of the photoactive yellow and green fluorescent proteins.

Electronic structure calculations of microhydrated model chromophores (in their deprotonated anionic forms) of the photoactive yellow and green fluorescent proteins (PYP and GFP) are reported. Electron-detachment and excitation energies as well as binding energies of mono- and dihydrated isomers are computed and analyzed. Microhydration has different effects on the excited and ionized states.

Electronic states of the benzene dimer: a simple case of complexity.

Electronic structure calculations of the excited states of the benzene dimer using equation-of-motion coupled-cluster method are reported. The calculations reveal large density of electronic states, including multiple valence, Rydberg, and mixed Rydberg-valence states. The calculations of the oscillator strengths for the transitions between the excimer state (i.

Spectroscopy and fragmentation of undercoordinated bromoiridates.

We report gas-phase electronic photodissociation spectra of the undercoordinated bromoiridate complexes IrBr(4)(-) and IrBr(5)(-) at photon energies from 1 to 5.6 eV. Both ions have open-shell ground states with low-symmetry structures.