A Comprehensive Computational Study on the Thermodynamics and Kinetics of Tetrahydrobiopterin Regeneration Process.

Tetrahydrobiopterin, one of the most crucial enzymatic cofactors acquired through biological synthesis and self-regeneration in the human body. During this process, it undergoes oxidation and deprotonation, forming quinonoid-dihydrobiopterin, which then tautomerizes to yield dihydrobiopterin. This study presents the thermodynamic and kinetic properties of each stage using theoretical calculations. Redox potentials and pKa values are determined using the Born-Haber cycle in implicit solvent models. Redox metabolites are characterized from calculated absorption spectra using time-dependent density functional theory. Rate constants for tautomerization steps are computed using Eyring's Transition State Theory, incorporating Wigner's tunneling correction. The N3 atom is identified as the most probable deprotonation site for H3B+. Spectral properties of intermediates are elucidated, highlighting key electronic transitions. Tautomerization steps occur through vibrational bending modes, and tunneling corrections significantly increase reaction rates. These findings provide a comprehensive understanding of the thermodynamics and kinetics of tetrahydrobiopterin regeneration, aiding in the modulation of its biological activity.

Unraveling the mystery of solvation-dependent fluorescence of fluorescein dianion using computational study.

Fluorescein, one of the brightest fluorescent dye molecules, is a widely used fluorophore for various applications from biomedicine to industry. The dianionic form of fluorescein is responsible for its high fluorescence quantum yield. Interestingly, the molecule was found to be nonfluorescent in the gas phase. This characteristic is attributed to the photodetachment process, which out-competes the fluorescence emission in the gas phase. In this work, we show that the calculated vertical and adiabatic detachment energies of fluorescein dianion in the gas and solvent phases account for the drastic differences observed in their fluorescence characteristics. The functional dependence of these detachment energies on the dianion's microsolvation was systematically investigated. The performance of different solvent models was also assessed. The higher thermodynamic stability of fluorescein dianion over the monoanion doublet in the solvent phase plays a crucial role in quenching photodetachment and activating the radiative channel with a high fluorescence quantum yield.

Controlled destabilization of caged circularized DNA oligonucleotides predicted by replica exchange molecular dynamics simulations.

Spatiotemporal control is a critical issue in the design of strategies for the photoregulation of oligonucleotide activity. Efficient uncaging, i.e., activation by removal of photolabile protecting groups (PPGs), often necessitates multiple PPGs. An alternative approach is based on circularization strategies, exemplified by intrasequential circularization, also denoted photo-tethering, as introduced in [Seyfried et al., Angew. Chem., Int. Ed., 2017, 56, 359]. Here, we develop a computational protocol, relying on replica exchange molecular dynamics (REMD), in order to characterize the destabilization of a series of circularized, caged DNA oligonucleotides addressed in the aforementioned study. For these medium-sized (32 nt) oligonucleotides, melting temperatures are computed, whose trend is in good agreement with experiment, exhibiting a large destabilization and, hence, reduction of the melting temperature of the order of ΔTm ∼ 30 K as compared with the native species. The analysis of free energy landscapes confirms the destabilization pattern experienced by the circularized oligonucleotides. The present study underscores that computational protocols that capture controlled destabilization and uncaging of oligonucleotides are promising as predictive tools in the tailored photocontrol of nucleic acids.

Strong Dopant-Dopant Electronic Coupling in Emissive Codoped Two Dimensional Metal Halide Hybrid.

Multimetallic halide hybrids are attractive for the fundamental understanding of interacting excitons. However, realizing halide hybrids that incorporate multiple heterometal centers has been synthetically challenging. This further limits access to gaining physical insight into the electronic coupling mechanism between the constituent metal halide units. Reported herein is an emissive heterometallic halide hybrid, synthesized by codoping (with Mn2+, Sb3+) a 2D host (C6H22N4CdCl6) hybrid, that shows strong dopant-dopant interaction. Here, C6H22N4Sb0.003Mn0.128Cd0.868Cl6 codoped hybrid shows weak green emission (Sb3+ dopant based) and strong orange emission (Mn2+ dopant based). The observed dominance of the Mn2+ dopant emission, arising due to efficient energy transfer between the distant dopants (Sb3+ → Mn2+), highlights strong dopant-dopant electronic coupling. DFT calculations, supporting the observed dopant-dopant interaction, suggest that the electronic coupling between the dopant units (Mn-Cl; Sb-Cl) is mediated by the 2D networked host structure. This work reports physical insight into the coupling mechanism of interacting excitons in multimetallic halide hybrids synthesized through a codoping strategy.

Molecular contacts in the Cren7-DNA complex: A quantitative investigation for electrostatic interaction.

The molecular association of proteins with nucleic acids leading to the formation of macromolecular complexes is a crucial step in several biological processes. Stabilization of these complexes involves electrostatic interactions between ion pairs (salt bridges) of nucleic acid phosphates and protein side chains. The crenarchaeal DNA binding protein, Cren7 plays a key role in the regulation of chromosomal structure and gene expression in eukaryotic extremophiles. However, the molecular contacts that occur at the interface of protein-DNA complexes and their contribution to the electrostatic interaction have not been fully elucidated. This work presents a quantitative description of the mechanism of the electrostatic interaction between the protein and DNA. We have identified a few residues located at the Cren7-DNA interface that could potentially be responsible for the interaction. Structural studies using circular dichroism indicate mutation of these surface residues minimally affect their structure and stability. The binding affinity of these mutants for the DNA duplexes was examined from reverse titration, biolayer interferometry, and fluorescence anisotropy measurements with calf thymus DNA, polynucleotides, and small DNA oligonucleotides. The resulting kinetic parameters highlight a difference in electrostatic interactions potentials exhibited by residues positioned at different locations of the protein-DNA interface. Computational studies attribute this difference to their surrounding atmosphere and energetic stabilization parameters. The biophysical approach described here can be extended for other proteins that play a crucial role in DNA bending and compaction, to properly evaluate the role of specific residues on the mechanisms of DNA binding.

Electronic Substitution Effect on the Ground and Excited State Properties of Indole Chromophore: A Computational Study.

Indole, being the main chromophore of amino acid tryptophan and several other biologically relevant molecules like serotonin, melatonin, has prompted considerable theoretical and experimental interest. The current work focuses on the investigation of substitution effect on the ground and excited electronic states of indole using computational quantum chemistry. Having three close-lying excited electronic states, the vibronic coupling effect becomes extremely important yet challenging for the photophysics and photochemistry of indole. Here, we have evaluated the performance of time-dependent density functional theory against available experimental and ab initio results from the literature. The electronic effects on the excited states of indole and indole derivatives e. g. tryptophan, serotonin and melatonin are reported. A bathochromic shift has been observed in the absorption spectrum for the La state. The absorption wavelength increases in the order of indole

Why intermolecular nitric oxide (NO) transfer? Exploring the factors and mechanistic aspects of NO transfer reaction.

Small molecule activation and their transfer reactions in biological or catalytic reactions are greatly influenced by the metal-centers and the ligand frameworks. Here, we report the metal-directed nitric oxide (NO) transfer chemistry in low-spin mononuclear {Co(NO)}8, [(12-TMC)CoIII(NO-)]2+ (1-CoNO, S = 0), and {Cr(NO)}5, ([(BPMEN)Cr(NO)(Cl)]+) (4-CrNO, S = 1/2) complexes. 1-CoNO transfers its bound NO moiety to a high-spin [(BPMEN)CrII(Cl2)] (2-Cr, S = 2) and generates 4-CrNOvia an associative pathway; however, we did not observe the reverse reaction, i.e., NO transfer from 4-CrNO to low-spin [(12-TMC)CoII]2+ (3-Co, S = 1/2). Spectral titration for NO transfer reaction between 1-CoNO and 2-Cr confirmed 1 : 1 reaction stoichiometry. The NO transfer rate was found to be independent of 2-Cr, suggesting the presence of an intermediate species, which was further supported experimentally and theoretically. The experimental and theoretical observations support the formation of µ-NO bridged intermediate species ({Cr-NO-Co}4+). Mechanistic investigations using 15N-labeled-15NO and tracking the 15N-atom established that the NO moiety in 4-CrNO is derived from 1-CoNO. Further, to investigate the factors deciding the NO transfer reactivity, we explored the NO transfer reaction between another high-spin CrII-complex, [(12-TMC)CrII(Cl)]+ (5-Cr, S = 2), and 1-CoNO, showing the generation of the low-spin [(12-TMC)Cr(NO)(Cl)]+ (6-CrNO, S = 1/2); however, again there was no opposite reaction, i.e., from Cr-center to Co-center. The above results advocate clearly that the NO transfer from Co-center generates thermally stable and low-spin and inert {Cr(NO)}5 complexes (4-CrNO & 6-CrNO) from high-spin and labile Cr-complexes (2-Cr & 5-Cr), suggesting a metal-directed NO transfer (cobalt to chromium, not chromium to cobalt). These results explicitly highlight that the NO transfer is strongly influenced by the labile/inert behavior of the metal-centers and/or thermal stability rather than the ligand architecture.

Multipolar Force Fields for Amide-I Spectroscopy from Conformational Dynamics of the Alanine Trimer.

The dynamics and spectroscopy of N-methyl-acetamide (NMA) and trialanine in solution are characterized from molecular dynamics simulations using different energy functions, including a conventional point charge (PC)-based force field, one based on a multipolar (MTP) representation of the electrostatics, and a semiempirical DFT method. For the 1D infrared spectra, the frequency splitting between the two amide-I groups is 10 cm-1 from the PC, 13 cm-1 from the MTP, and 47 cm-1 from self-consistent charge density functional tight-binding (SCC-DFTB) simulations, compared with 25 cm-1 from experiment. The frequency trajectory required for the frequency fluctuation correlation function (FFCF) is determined from individual normal mode (INM) and full normal mode (FNM) analyses of the amide-I vibrations. The spectroscopy, time-zero magnitude of the FFCF C(t = 0), and the static component Δ02 from simulations using MTP and analysis based on FNM are all consistent with experiments for (Ala)3. Contrary to this, for the analysis excluding mode-mode coupling (INM), the FFCF decays to zero too rapidly and for simulations with a PC-based force field, the Δ02 is too small by a factor of two compared with experiments. Simulations with SCC-DFTB agree better with experiment for these observables than those from PC-based simulations. The conformational ensemble sampled from simulations using PCs is consistent with the literature (including PII, ß, αR, and αL), whereas that covered by the MTP-based simulations is dominated by PII with some contributions from ß and αR. This agrees with and confirms recently reported Bayesian-refined populations based on 1D infrared experiments. FNM analysis together with a MTP representation provides a meaningful model to correctly describe the dynamics of hydrated trialanine.

Correction: In silico decryption of serotonin-receptor binding: local non-covalent interactions and long-range conformational changes.

[This corrects the article DOI: 10.1039/D0RA05559J.].

Non-conventional force fields for applications in spectroscopy and chemical reaction dynamics.

Extensions and improvements of empirical force fields are discussed in view of applications to computational vibrational spectroscopy and reactive molecular dynamics simulations. Particular focus is on quantitative studies, which make contact with experiments and provide complementary information for a molecular-level understanding of processes in the gas phase and in solution. Methods range from including multipolar charge distributions to reproducing kernel Hilbert space approaches and machine learned energy functions based on neural networks.

In silico decryption of serotonin-receptor binding: local non-covalent interactions and long-range conformational changes.

Serotonin-receptor binding is the key step in the process behind serotonin functionality, including several psychological and physiological behaviours. This study is focused on identifying the main non-covalent interactions controlling the stability of serotonin-receptor complexes as well as the main conformational changes in the receptor due to serotonin-receptor binding using classical molecular dynamics simulations and quantum chemical calculations. A qualitative analysis based on two order parameters ((i) the centre of mass distance and (ii) the angle between the surface normals of each aromatic residue and serotonin in the binding site) on the serotonin-receptor complex trajectory suggests that the T-type stacking interaction is predominant in the binding site. Quantum chemical calculations of the stacking interaction energy provide the quantitative contributions of important aromatic residues to the stabilization of the complex. Furthermore, a three body stacking interaction (named 'L'-type) was observed and likely contributes to the stability of the complex. Direct and water-mediated hydrogen bonding between the residues in the binding site and serotonin contributes to the complex stability. Principal component analysis of the molecular dynamics simulation trajectory of the serotonin-receptor complex and the apo-receptor in water indicates that the whole receptor is significantly stabilized due to serotonin binding. An analysis based on the dynamic cross correlation function reflects the strong correlation between trans-membrane (TM)3, TM5, TM6 (containing residues responsible for the stacking interaction and hydrogen bonding) and mini-G0 which may participate in signal transduction leading to the functionality of serotonin.

Theoretical insights into the formation and stability of radical oxygen species in cryptochromes.

Cryptochrome is a blue-light absorbing flavoprotein containing a flavin adenine dinucleotide (FAD) cofactor. FAD can accept up to two electrons and two protons, which can be subsequently transferred to substrates present in the binding pocket. It is well known that reactive oxygen species are generated when triplet molecular oxygen is present in the cavity. Here, we investigate the formation and stability of radical oxygen species in Drosophila melanogaster cryptochrome using molecular dynamics simulations and electronic structure calculations. We find that the superoxide and hydroxyl radicals in doublet spin states are stabilized in the pocket due to the attractive electrostatic interactions and hydrogen bonding with partially reduced FAD. These findings validate from a molecular dynamics perspective that [FAD˙--HO2˙] or [FADH˙-O2˙-] can be alternative radical pairs at the origin of magnetoreception.

Azobenzene as a photoregulator covalently attached to RNA: a quantum mechanics/molecular mechanics-surface hopping dynamics study.

The photoregulation of nucleic acids by azobenzene photoswitches has recently attracted considerable interest in the context of emerging biotechnological applications. To understand the mechanism of photoinduced isomerisation and conformational control in these complex biological environments, we employ a Quantum Mechanics/Molecular Mechanics (QM/MM) approach in conjunction with nonadiabatic Surface Hopping (SH) dynamics. Two representative RNA-azobenzene complexes are investigated, both of which contain the azobenzene chromophore covalently attached to an RNA double strand via a ß-deoxyribose linker. Due to the pronounced constraints of the local RNA environment, it is found that trans-to-cis isomerization is slowed down to a time scale of ∼10-15 picoseconds, in contrast to 500 femtoseconds in vacuo, with a quantum yield reduced by a factor of two. By contrast, cis-to-trans isomerization remains in a sub-picosecond regime. A volume-conserving isomerization mechanism is found, similarly to the pedal-like mechanism previously identified for azobenzene in solution phase. Strikingly, the chiral RNA environment induces opposite right-handed and left-handed helicities of the ground-state cis-azobenzene chromophore in the two RNA-azobenzene complexes, along with an almost completely chirality conserving photochemical pathway for these helical enantiomers.

Solvent Composition Drives the Rebinding Kinetics of Nitric Oxide to Microperoxidase.

The rebinding kinetics of NO after photodissociation from microperoxidase (Mp-9) is studied in different solvent environments. In mixed glycerol/water (G/W) mixtures the dissociating ligand rebinds with a yield close to 1 due to the cavities formed by the solvent whereas in pure water the ligand can diffuse into the solvent after photodissociation. In the G/W mixture, only geminate rebinding on the sub-picosecond and 5 ps time scales was found and the rebinding fraction is unity which compares well with available experiments. Contrary to that, simulations in pure water find two time scales - ~10 ps and ~200 ps - indicating that both, geminate rebinding and rebinding after diffusion of NO in the surrounding water contribute. The rebinding fraction is around 0.63 within 1 ns which is in stark contrast with experiment. Including ions (Na and Cl) at 0.15 M concentration in water leads to rebinding kinetics tending to that in the glycerol/water mixture and yields agreement with experiments. The effect of temperature is also probed and found to be non-negligible. The present simulations suggest that NO rebinding in Mp is primarily driven by thermal fluctuations which is consistent with recent resonance Raman spectroscopy experiments and simulations on MbNO.

Vibrational Stark spectroscopy for assessing ligand-binding strengths in a protein.

Nitrile groups are potentially useful spectroscopic probes in the infrared to characterize the binding and dynamics of ligands in proteins. This opens the possibility of locating and determining the binding mode of suitably labelled ligands in proteins based on optical spectroscopy, without the need for determining an X-ray structure. However, relating structure and spectroscopy requires means to accurately compute infrared spectra. This is investigated for benzonitrile (PhCN) in water, wild type (WT) and two lysozyme mutants in solution. The force field is validated by comparing with experimental data for benzonitrile in water which is the basis for computing the Stark shift and time scale for spectral diffusion of PhCN in WT and the L99A and L99G mutants of T4 lysozyme. The 1-d spectra for PhCN in WT and the two mutant proteins differ in their maximum absorption by up to 4 cm-1, which reflects the modified electrostatic environments in the three proteins. It is also tested whether extending from 1-d to 2-d infrared spectroscopy provides further discrimination in the ligand-binding modes. First, for PhCN in solution the frequency fluctuation correlation function (FFCF) decays to zero at short times whereas in the protein a pronounced static inhomogeneous component is found. Secondly, the decay time of the FFCF for the mutant to which PhCN binds most strongly has the longest decay time. It is demonstrated explicitly that the ligand-binding free energy with respect to the three protein variants correlates with the Stark shift. This makes 1-d infrared spectroscopy together with computations a valuable tool for characterizing binding modes and potentially binding locations in proteins.

In Search of an Efficient Photoswitch for Functional RNA: Design Principles from a Microscopic Analysis of Azobenzene-linker-RNA Dynamics with Different Linkers.

The design of optimal photoswitches to regulate nucleic acid functionality is a considerable challenge. Azobenzene switches that are covalently bound to the nucleic acid backbone are a paradigm example that has been studied using different types of linker species connecting the chromophore to the backbone. To support experimental efforts to construct optimal azobenzene-linker-RNA combinations, we introduce here a systematic approach for theoretical analysis, which provides criteria for the local embedding of the chromophore via a chosen linker. Using a local reference frame adapted to the chromophore, quantitative measures are provided for (i) the propensity of stacking in competition with a drift toward the minor or major groove, (ii) the tendency to disrupt the native hydrogen bond network, (iii) the structural flexibility of the chromophore-linker combination, and (iv) the correlations with the presence of a base in the opposite strand. Large differences in structural stability between the trans and cis forms of the azobenzene chromophore, according to these criteria, indicate good functionality and lead to significant differences in melting temperatures. In particular, a recently synthesized deoxyribose linker proves optimal within the set of azobenzene-linker-RNA combinations considered.

Reversible photoswitching of RNA hybridization at room temperature with an azobenzene C-nucleoside.

Photoregulation of RNA remains a challenging task as the introduction of a photoswitch entails changes in the shape and the stability of the duplex that strongly depend on the chosen linker strategy. Herein, the influence of a novel nucleosidic linker moiety on the photoregulation efficiency of azobenzene is investigated. To this purpose, two azobenzene C-nucleosides were stereoselectively synthesized, characterized, and incorporated into RNA oligonucleotides. Spectroscopic characterization revealed a reversible and fast switching process, even at 20 °C, and a high thermal stability of the respective cis isomers. The photoregulation efficiency of RNA duplexes upon trans-to-cis isomerization was investigated by using melting point studies and compared with the known D-threoninol-based azobenzene system, revealing a photoswitching amplitude of the new residues exceeding 90 % even at room temperature. Structural changes in the duplexes upon photoisomerization were investigated by using MM/MD calculations. The excellent photoswitching performance at room temperature and the high thermal stability make these new azobenzene residues promising candidates for in-vivo and nanoarchitecture photoregulation applications of RNA.

Infrared Absorption Spectra of Jahn-Teller Systems: Application to the Transition-Metal Trifluorides MnF3 and NiF3.

The theory for the calculation of vibronic absorption spectra within a Jahn-Teller (JT) active electronic state from first principles has been developed. The infrared absorption spectra of the 5E' ground state, the low-lying 5E″ excited state of MnF3, and the 4E' state of NiF3 have been computed and analyzed. Dipole moment derivatives have been determined by a linear-plus-quadratic expansion of nuclear dipole moment functions in the JT-active coordinates. Electronic transition dipole moments have been taken into account in the Condon approximation in the diabatic representation. The initial and final vibronic states have been expanded in a product of diabatic electronic states and vibrational basis functions. The effect of spin-orbit coupling on the vibronic infrared spectra of these molecules in their JT-active electronic states has been investigated, by employing the Breit-Pauli spin-orbit operator. The effect of temperature on the vibronic infrared spectra has also been explored. These results represent the first theoretical study of vibronic infrared spectra of JT-active states in transition metal compounds.

Ab initio study of dynamical E × e Jahn-Teller and spin-orbit coupling effects in the transition-metal trifluorides TiF3, CrF3, and NiF3.

Multiconfiguration ab initio methods have been employed to study the effects of Jahn-Teller (JT) and spin-orbit (SO) coupling in the transition-metal trifluorides TiF(3), CrF(3), and NiF(3), which possess spatially doubly degenerate excited states ((M)E) of even spin multiplicities (M = 2 or 4). The ground states of TiF(3), CrF(3), and NiF(3) are nondegenerate and exhibit minima of D(3h) symmetry. Potential-energy surfaces of spatially degenerate excited states have been calculated using the state-averaged complete-active-space self-consistent-field method. SO coupling is described by the matrix elements of the Breit-Pauli operator. Linear and higher order JT coupling constants for the JT-active bending and stretching modes as well as SO-coupling constants have been determined. Vibronic spectra of JT-active excited electronic states have been calculated, using JT Hamiltonians for trigonal systems with inclusion of SO coupling. The effect of higher order (up to sixth order) JT couplings on the vibronic spectra has been investigated for selected electronic states and vibrational modes with particularly strong JT couplings. While the weak SO couplings in TiF(3) and CrF(3) are almost completely quenched by the strong JT couplings, the stronger SO coupling in NiF(3) is only partially quenched by JT coupling.

Effect of surface modes on the six-dimensional molecule-surface scattering dynamics of H2-Cu(100) and D2-Cu(111) systems.

We include the phonon modes originating from the three layers of Cu(100)/Cu(111) surface atoms on the dynamics of molecular [H(2)(v,j)/D(2)(v,j)] degrees of freedom (DOFs) through a mean field approach, where the surface temperature is incorporated into the effective Hamiltonian (potential) either by considering Boltzmann probability (BP) or by including the Bose-Einstein probability (BEP) factor for the initial state distribution of the surface modes. The formulation of effective potential has been carried out by invoking the expression of transition probabilities for phonon modes known from the "stochastic" treatment of linearly forced harmonic oscillator (LFHO). We perform four-dimensional (4D⊗2D) as well as six-dimensional (6D) quantum dynamics on a parametrically time and temperature-dependent effective Hamiltonian to calculate elastic/inelastic scattering cross-section of the scattered molecule for the H(2)(v,j)-Cu(100) system, and dissociative chemisorption-physisorption for both H(2)(v,j)-Cu(100) and D(2)(v,j)-Cu(111) systems. Calculated sticking probabilities by either 4D⊗2D or 6D quantum dynamics on an effective potential constructed by using BP factor for the initial state distribution of the phonon modes could not show any surface temperature dependence. In the BEP case, (a) both 4D⊗2D and 6D quantum dynamics demonstrate that the phonon modes of the Cu(100) surface affect the state-to-state transition probabilities of the scattered H(2) molecule substantially, and (b) the sticking probabilities due to the collision of H(2) on Cu(100) and D(2) on Cu(111) surfaces show noticeable and substantial change, respectively, as function of surface temperature only when the quantum dynamics of all six molecular DOFs are treated in a fully correlated manner (6D).