Quantum Chemical Microsolvation by Automated Water Placement.
Ontology highlight
ABSTRACT:
SUBMITTER: Steiner M
PROVIDER: S-EPMC8005176 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:An organic radical monohydrate complex is detected in vacuum isolation at low temperature by FTIR supersonic jet spectroscopy for the first time. It is shown to exhibit a rich conformational and vibrational coupling dynamics, which can be drastically reduced by appropriate isotope substitution. Its detection with a new gas recycling infrared spectrometer demonstrates the thermal metastability of the gaseous TEMPO radical even under humid gas conditions. Compared to its almost isoelectronic and isostructural, closed shell ketone analogue, the hydrogen bond of the solvating water is found to be less directional, but stronger and more strongly downshifting the bonded water OH stretch vibration. A second solvent water directs the first one into a metastable hydrogen bond position to solvate the nitrogen center and the first water at the same time.
| S-EPMC8456822 | biostudies-literature
Project description:We evaluate the performance of the automated fragmentation quantum mechanics/molecular mechanics approach (AF-QM/MM) on the calculation of protein and nucleic acid NMR chemical shifts. The AF-QM/MM approach models solvent effects implicitly through a set of surface charges computed using the Poisson-Boltzmann equation, and it can also be combined with an explicit solvent model through the placement of water molecules in the first solvation shell around the solute; the latter substantially improves the accuracy of chemical shift prediction of protons involved in hydrogen bonding with solvent. We also compare the performance of AF-QM/MM on proteins and nucleic acids with two leading empirical chemical shift prediction programs SHIFTS and SHIFTX2. Although the empirical programs outperform AF-QM/MM in predicting chemical shifts, the differences are in some cases small, and the latter can be applied to chemical shifts on biomolecules which are outside the training set employed by the empirical programs, such as structures containing ligands, metal centers, and non-standard residues. The AF-QM/MM described here is implemented in version 5 of the SHIFTS software, and is fully automated, so that only a structure in PDB format is required as input.
| S-EPMC6556433 | biostudies-literature
Project description:We present here the first application of the quantum chemical topology force field FFLUX to condensed matter simulations. FFLUX offers many-body potential energy surfaces learnt exclusively from ab initio data using Gaussian process regression. FFLUX also includes high-rank, polarizable multipole moments (up to quadrupole moments in this work) that are learnt from the same ab initio calculations as the potential energy surfaces. Many-body effects (where a body is an atom) and polarization are captured by the machine learning models. The choice to use machine learning in this way allows the force field's representation of reality to be improved (e.g., by including higher order many-body effects) with little detriment to the computational scaling of the code. In this manner, FFLUX is inherently future-proof. The "plug and play" nature of the machine learning models also ensures that FFLUX can be applied to any system of interest, not just liquid water. In this work we study liquid water across a range of temperatures and compare the predicted bulk properties to experiment as well as other state-of-the-art force fields AMOEBA(+CF), HIPPO, MB-Pol and SIBFA21. We find that FFLUX finds a place amongst these.
| S-EPMC9476653 | biostudies-literature
Project description:The effect of microsolvation on excited-state proton transfer (ESPT) reaction of 3-hydroxyflavone (3HF) and its inclusion complex with ?-cyclodextrin (?-CD) was studied using computational approaches. From molecular dynamics simulations, two possible inclusion complexes formed by the chromone ring (C-ring, Form I) and the phenyl ring (P-ring, Form II) of 3HF insertion to ?-CD were observed. Form II is likely more stable because of lower fluctuation of 3HF inside the hydrophobic cavity and lower water accessibility to the encapsulated 3HF. Next, the conformation analysis of these models in the ground (S0) and the first excited (S1) states was carried out by density functional theory (DFT) and time-dependent DFT (TD-DFT) calculations, respectively, to reveal the photophysical properties of 3HF influenced by the ?-CD. The results show that the intermolecular hydrogen bonding (interHB) between 3HF and ?-CD, and intramolecular hydrogen bonding (intraHB) within 3HF are strengthened in the S1 state confirmed by the shorter interHB and intraHB distances and the red-shift of O-H vibrational modes involving in the ESPT process. The simulated absorption and emission spectra are in good agreement with the experimental data. Significantly, in the S1 state, the keto form of 3HF is stabilized by ?-CD, explaining the increased quantum yield of keto emission of 3HF when complexing with ?-CD in the experiment. In the other word, ESPT of 3HF is more favorable in the ?-CD hydrophobic cavity than in aqueous solution.
| S-EPMC7914428 | biostudies-literature
Project description:Theoretical approaches for predicting physicochemical properties are valuable tools for accelerating the drug discovery process. In this work, quantum chemical methods are used to predict water-octanol partition coefficients as a part of the SAMPL6 blind challenge. The SMD continuum solvent model was employed with MP2 and eight DFT functionals in conjunction with correlation consistent basis sets to determine the water-octanol transfer free energy. Several tactics towards improving the predictions of the partition coefficient were examined, including increasing the quality of basis sets, considering tautomerization, and accounting for inhomogeneities in the water and n-octanol phases. Evaluation of these various schemes highlights the impact of modeling approaches across different methods. With the inclusion of tautomers and adjustments to the permittivity constants, the best predictions were obtained with smaller basis sets and the O3LYP functional, which yielded an RMSE of 0.79 logP units. The results presented correspond to the SAMPL6 logP submission IDs: DYXBT, O7DJK, and AHMTF.
| S-EPMC8690632 | biostudies-literature
Project description:Quantum indistinguishability plays a crucial role in many low-energy physical phenomena, from quantum fluids to molecular spectroscopy. It is, however, typically ignored in most high-temperature processes, particularly for ionic coordinates, implicitly assumed to be distinguishable, incoherent, and thus well approximated classically. We explore enzymatic chemical reactions involving small symmetric molecules and argue that in many situations a full quantum treatment of collective nuclear degrees of freedom is essential. Supported by several physical arguments, we conjecture a "quantum dynamical selection" (QDS) rule for small symmetric molecules that precludes chemical processes that involve direct transitions from orbitally nonsymmetric molecular states. As we propose and discuss, the implications of the QDS rule include (i) a differential chemical reactivity of para- and orthohydrogen, (ii) a mechanism for inducing intermolecular quantum entanglement of nuclear spins, (iii) a mass-independent isotope fractionation mechanism, (iv) an explanation of the enhanced chemical activity of "reactive oxygen species", (v) illuminating the importance of ortho-water molecules in modulating the quantum dynamics of liquid water, and (vi) providing the critical quantum-to-biochemical linkage in the nuclear spin model of the (putative) quantum brain, among others.
| S-EPMC5960291 | biostudies-literature
Project description:BackgroundHydrogen bonds play a major role in the stabilization of protein-ligand complexes. The ability of a functional group to form them depends on the position of its hydrogen atoms. An accurate knowledge of the positions of hydrogen atoms in proteins is therefore important to correctly identify hydrogen bonds and their properties. The high mobility of hydrogen atoms introduces several degrees of freedom: Tautomeric states, where a hydrogen atom alters its binding partner, torsional changes where the position of the hydrogen atom is rotated around the last heavy-atom bond in a residue, and protonation states, where the number of hydrogen atoms at a functional group may change. Also, side-chain flips in glutamine and asparagine and histidine residues, which are common crystallographic ambiguities must be identified before structure-based calculations can be conducted.ResultsWe have implemented a method to determine the most probable hydrogen atom positions in a given protein-ligand complex. Optimality of hydrogen bond geometries is determined by an empirical scoring function which is used in molecular docking. This allows to evaluate protein-ligand interactions with an established model. Also, our method allows to resolve common crystallographic ambiguities such as as flipped amide groups and histidine residues. To ensure high speed, we make use of a dynamic programming approach.ConclusionOur results were checked against selected high-resolution structures from an external dataset, for which the positions of the hydrogen atoms have been validated manually. The quality of our results is comparable to that of other programs, with the advantage of being fast enough to be applied on-the-fly for interactive usage or during score evaluation.
| S-EPMC3225823 | biostudies-literature
Project description:Quantum chemical methods now permit the prediction of many spectroscopic observables in proteins and related model systems, in addition to electrostatic properties, which are found to be in excellent accord with those determined from experiment. I discuss the developments over the past decade in these areas, including predictions of nuclear magnetic resonance chemical shifts, chemical shielding tensors, scalar couplings and hyperfine (contact) shifts, the isomer shifts and quadrupole splittings in Mössbauer spectroscopy, molecular energies and conformations, as well as a range of electrostatic properties, such as charge densities, the curvatures, Laplacians and Hessians of the charge density, electrostatic potentials, electric field gradients and electrostatic field effects. The availability of structure/spectroscopic correlations from quantum chemistry provides a basis for using numerous spectroscopic observables in determining aspects of protein structure, in determining electrostatic properties which are not readily accessible from experiment, as well as giving additional confidence in the use of these techniques to investigate questions about chemical bonding and chemical reactions.
| S-EPMC1569496 | biostudies-literature
Project description:The ability to tune the optoelectronic properties of quantum dots (QDs) makes them ideally suited for the use as fluorescence sensing probes. The vast structural diversity in terms of the composition and size of QDs can make designing a QD for a specific sensing application a challenging process. Quantum chemical calculations have the potential to aid this process through the characterization of the properties of QDs, leading to their in silico design. This is explored in the context of QDs for the fluorescence sensing of dopamine based upon density functional theory and time-dependent density functional theory (TDDFT) calculations. The excited states of hydrogenated carbon, silicon, and germanium QDs are characterized through TDDFT calculations. Analysis of the molecular orbital diagrams for the isolated molecules and calculations of the excited states of the dopamine-functionalized quantum dots establish the possibility of a photoinduced electron-transfer process by determining the relative energies of the electronic states formed from a local excitation on the QD and the lowest QD → dopamine electron-transfer state. The results suggest that the Si165H100 and Ge84H64 QDs have the potential to act as fluorescent markers that could distinguish between the oxidized and reduced forms of dopamine, where the fluorescence would be quenched for the oxidized form. The work contributes to a better understanding of the optical and electronic behavior of QD-based sensors and illustrates how quantum chemical calculations can be used to inform the design of QDs for specific fluorescent sensing applications.
| S-EPMC9125561 | biostudies-literature
Project description:The separation of colloidal nanocrystals from their original synthesis medium is an essential process step towards their application, however, the costs on a preparative scale are still a constraint. A new combination of approaches for the purification of hydrophobic Quantum Dots is presented, resulting in an efficient scalable process in regard to time and solvent consumption, using common laboratory equipment and low-cost materials. The procedure is based on a combination of solvent-induced adhesion and solid phase extraction. The platform allows the transition from manual handling towards automation, yielding an overall purification performance similar to one conventional batch precipitation/centrifugation step, which was investigated by thermogravimetry and gas chromatography. The distinct miscibility gaps between surfactants used as nanoparticle capping agents, original and extraction medium are clarified by their phase diagrams, which confirmed the outcome of the flow chemistry process. Furthermore, the solubility behavior of the Quantum Dots is put into context with the Hansen solubility parameters framework to reasonably decide upon appropriate solvent types.
| S-EPMC9230973 | biostudies-literature