Torsional Barrier Research Articles

Docking, MD Simulations, and DFT Calculations: Assessing W254's Function and Sartan Binding in Furin.

Furins are serine endoproteases that are involved in many biological processes, where they play important roles in normal metabolism, in the activation of various pathogens, while they are a target for therapeutic intervention. Dichlorophenyl-pyridine "BOS" compounds are well known drugs that are used as inhibitors of human furin by an induced-fit mechanism, in which tryptophan W254 in the furin catalytic cleft acts as a molecular transition energy gate. The binding of "BOS" drug into the active center of furin has been computationally studied using the density functional theory (DFT) and ONIOM multiscaling methodologies. The binding enthalpies of the W254 with the furin-BOS is -32.8 kcal/mol ("open") and -18.8 kcal/mol ("closed"), while the calculated torsion barrier was found at 30 kcal/mol. It is significantly smaller than the value of previous MD calculations due to the relaxation of the environment, i.e., nearby groups of the W254, leading to the reduction of the energy demands. The significant lower barrier explains the experimental finding that the dihedral barrier of W254 is overcome. Furthermore, sartans were studied to evaluate their potential as furin inhibitors. Sartans are AT1 antagonists, and they effectively inhibit the hypertensive effects induced by the peptide hormone Angiotensin II. Here, they have been docked into the cavity to evaluate their effect on the BOS ligand via docking and molecular dynamics simulations. A consistent binding of sartans within the cavity during the simulation was found, suggesting that they could act as furin inhibitors. Finally, sartans interact with the same amino acids as W254, leading to a competitive binding that may influence the pharmacological efficacy and potential drug interactions of sartans.

Self diffusion, viscosity, and surface tension estimations of amines by using AUA4 force field

Accurate and efficient molecular dynamic simulation of amine functional group is crucial for designing improved carbon dioxide absorption processes, as thermodynamic and transport properties can be concurrently calculated with molecular-level insight. The exploration of these properties has been limited, and all-atom force fields have struggled to cope with the dynamic and equilibrium characteristics of amines, especially monoethanolamine, which possess and exceptionally low self-diffusivity. In response to this situation, we propose using an anisotropic united atom (AUA4) force field, which strikes a balance between precision and performance allowing to predict the key transport and equilibrium properties involved in mass transfer units. A total of 7 amines were included in this study. Among the main results observed in this work, there was excellent recreation of density. The surface tension evidenced performance similar to other transferable force fields with a general positive deviation of 20%. Regarding transport properties, methylamine and linear alkylamines shows moderate uniform deviations. Trimethylamne, being the only one tertiary amine, exhibited higher deviations than the other amines. In contrast, excellent results were obtained for ET-DI, while significant deviations were found for MEA. Nevertheless, in light of previous studies on this alkanolamine, these deviations appear promising. Finally, we were able to achieve the best predictions of the currently available force fields for ethanolamine by increasing its torsional barriers. This allowed us to accurately reproduce its low self-diffusion and viscosity while maintaining its main structural features.

The Heavy Atom Structure, "cis effect" on Methyl Internal Rotation, and 14N Nuclear Quadrupole Coupling of 1-Cyanopropene from Quantum Chemical and Microwave Spectroscopic Analysis.

The microwave spectrum of 1-cyanopropene (crotonitrile) was remeasured using two pulsed molecular jet Fourier transform microwave spectrometers operating from 2.0 to 40.0 GHz. The molecule exists in two isomer forms, E and Z, with respect to the orientation between the methyl and the cyano groups. The spectrum of the Z isomer is more intense. Due to internal rotation of the methyl group, doublets containing A and E torsional species were found for all rotational transitions. Hyperfine splittings arising from the 14N nuclear quadrupole coupling were resolved. The heavy atom structure of the Z isomer was determined by observation of 13C and 15N isotopologue spectra in natural abundances. The experimental results were supported by quantum chemistry. The complex spectral patterns were analyzed and fitted globally, and the barriers to methyl internal rotation are determined to be 478.325(28) cm-1 and 674.632(76) cm-1 for the Z and E isomers, respectively. The non-bonded intramolecular electrostatic attraction between the methyl group and the 1-cyano substituent overcomes steric hindrance, leading to higher stability of the Z isomer. The consequence is a slight opening of 3.2° of the C(1)-C(2)-C(3) angle and a radical decrease of the methyl torsional barrier in the Z isomer due to steric repulsion.

Coupled internal rotations and 14N quadrupole hyperfine structure of 2,4-dimethylpyrrole investigated by microwave spectroscopy and quantum chemistry.

The microwave spectrum of 2,4-dimethylpyrrole was investigated using a Fourier-transform microwave spectrometer in a supersonic expansion. Torsional splittings arising from two inequivalent methyl internal rotors in combination with hyperfine splittings due to the nuclear quadrupole coupling of the 14N nucleus were observed. The experiments were accompanied by quantum chemical calculations. A total of 1561 rotational lines were assigned and fitted in global fits using the programs XIAM and BELGI-Cs-2Tops-hyperfine, both achieved the measurement accuracy of 4kHz. Local separate fits were also performed to verify the correctness of the assignment. Accurate experimental molecular and internal rotation parameters could be deduced and compared to the calculated ones. The barrier to internal rotation of the 2-methyl rotor was determined to be 277.830(26) cm-1, essentially the same as the value of about 280cm-1 found for 2-methylpyrrole but lower than the value of 317cm-1 found for 2,5-dimethylpyrrole. The torsional barrier value of the 4-methyl rotor is 262.210(27) cm-1, slightly higher than the value of 246cm-1 found for 3-methylpyrrole. Benchmarking the rotational constants for 2,4- and 2,5-dimethylpyrrole revealed that the MP2/6-31G(d,p) level could be helpful to guide the assignment of microwave spectra of pyrrole derivatives.

The Far-Infrared Spectrum of Methoxymethanol (CH3-O-CH2OH): A Theoretical Study.

Methoxymethanol (CH3OCH2OH), an oxygenated volatile organic compound of low stability detected in the interstellar medium, represents an example of nonrigid organic molecules showing various interacting and inseparable large-amplitude motions. The species discloses a relevant coupling among torsional modes, strong enough to prevent complete assignments using effective Hamiltonians of reduced dimensionality. Theoretical models for rotational spectroscopy can improve if they treat three vibrational coordinates together. In this paper, the nonrigid properties and the far-infrared region are analyzed using highly correlated ab initio methods and a three-dimensional vibrational model. The molecule displays two gauche-gauche (CGcg and CGcg') and one trans-gauche (Tcg) conformers, whose relative energies are very small (CGcg/CGcg'/Tcg = 0.0:641.5:792.7 cm-1). The minima are separated by relatively low barriers (1200-1500 cm-1), and the corresponding methyl torsional barriers V 3 are estimated to be 595.7, 829.0, and 683.7 cm-1, respectively. The ground vibrational state rotational constants of the most stable geometry have been computed to be A 0 = 17233.99 MHz, B 0 = 5572.58 MHz, and C 0 = 4815.55 MHz, at ΔA 0 = -3.96 MHz, ΔB 0 = 4.76 MHz, and ΔC 0 = 2.51 MHz from previous experimental data. Low-energy levels and their tunneling splittings are determined variationally up to 700 cm-1. The A/E splitting of the ground vibrational state was computed to be 0.003 cm-1, as was expected given the methyl torsional barrier (∼600 cm-1). The fundamental levels (100), (010), and (001) are predicted at 132.133 and 132.086 cm-1 (methyl torsion), 186.507 and 186.467 cm-1 (O-CH3 torsion), and 371.925 and 371.950 cm-1 (OH torsion), respectively.

Structure and Spectroscopic Insights for CH3PCO Isomers: A High-Level Quantum Chemical Study.

The exploration of phosphorus-bearing species stands as a prolific field in current astrochemical research, particularly within the context of prebiotic chemistry. Herein, we have employed high-level quantum chemistry methodologies to predict the structure and spectroscopic properties of isomers composed of a methyl group and three P, C, and O atoms. We have computed relative and dissociation energies, as well as rotational, rovibrational, and torsional parameters using the B2PLYPD3 functional and the explicitly correlated coupled cluster CCSD(T)-F12b method. Based upon our study, all the isomers exhibit a bent heavy atom skeleton with CH3PCO being the most stable structure, regardless of the level theory employed. Following in energy, we found four high-energy isomers, namely, CH3OCP, CH3CPO, CH3COP, and CH3OPC. The computed adiabatic dissociation energies support the stability of all [CH3, P, C, O] isomers against fragmentation into CH3 and [P, C, O]. Torsional barrier heights associated with the methyl internal rotation for each structure have been computed to evaluate the occurrence of possible A-E splittings in the rotational spectra. For the most stable isomer, CH3PCO, we found a V3 barrier of 82 cm-1, which is slightly larger than that obtained experimentally for the N-counterpart, CH3NCO, yet still very low. Therefore, the analysis of its rotational spectrum can be anticipated as a challenging task owing to the effect of the CH3 internal rotation. The complete set of spectroscopic constants and transition frequencies reported here for the most stable isomer, CH3PCO, is intended to facilitate eventual laboratory searches.

Enhancing torsional sampling using fully adaptive simulated tempering.

Enhanced sampling algorithms are indispensable when working with highly disconnected multimodal distributions. An important application of these is the conformational exploration of particular internal degrees of freedom of molecular systems. However, despite the existence of many commonly used enhanced sampling algorithms to explore these internal motions, they often rely on system-dependent parameters, which negatively impact efficiency and reproducibility. Here, we present fully adaptive simulated tempering (FAST), a variation of the irreversible simulated tempering algorithm, which continuously optimizes the number, parameters, and weights of intermediate distributions to achieve maximally fast traversal over a space defined by the change in a predefined thermodynamic control variable such as temperature or an alchemical smoothing parameter. This work builds on a number of previously published methods, such as sequential Monte Carlo, and introduces a novel parameter optimization procedure that can, in principle, be used in any expanded ensemble algorithms. This method is validated by being applied on a number of different molecular systems with high torsional kinetic barriers. We also consider two different soft-core potentials during the interpolation procedure and compare their performance. We conclude that FAST is a highly efficient algorithm, which improves simulation reproducibility and can be successfully used in a variety of settings with the same initial hyperparameters.

Activation and friction in enzymatic loop opening and closing dynamics

Protein loop dynamics have recently been recognized as central to enzymatic activity, specificity and stability. However, the factors controlling loop opening and closing kinetics have remained elusive. Here, we combine molecular dynamics simulations with string-method determination of complex reaction coordinates to elucidate the molecular mechanism and rate-limiting step for WPD-loop dynamics in the PTP1B enzyme. While protein conformational dynamics is often represented as diffusive motion hindered by solvent viscosity and internal friction, we demonstrate that loop opening and closing is activated. It is governed by torsional rearrangement around a single loop peptide group and by significant friction caused by backbone adjustments, which can dynamically trap the loop. Considering both torsional barrier and time-dependent friction, our calculated rate constants exhibit very good agreement with experimental measurements, reproducing the change in loop opening kinetics between proteins. Furthermore, we demonstrate the applicability of our results to other enzymatic loops, including the M20 DHFR loop, thereby offering prospects for loop engineering potentially leading to enhanced designs.

Low barriers to internal rotation in the microwave spectrum of 2,5-dimethylfluorobenzene.

We investigated the rotational spectrum of 2,5-dimethylfluorobenzene containing coupled large amplitude motions of two methyl groups in the frequency range from 2 to 26.5GHz using a pulsed molecular jet Fourier transform microwave spectrometer. The internal rotation of two inequivalent methyl groups with low torsional barriers (around 16 and 226cm-1) causes splittings of all rotational transitions into quintets with separations of up to hundreds of MHz between the torsional components. Spectral analysis and modeling of the observed splittings were performed using the programs XIAM and BELGI-Cs-2Tops, whereby the latter achieved measurement accuracy. The methyl internal rotation can be used to examine the electronic and steric environments around the methyl group because they affect the methyl torsional barrier. Electronic properties play a particularly important role in aromatic molecules in the presence of a π-conjugated double bond system. The experimental results were compared with those of quantum chemistry. Benchmark calculations resulted in the conclusion that the B3LYP-D3BJ/6-311++G(d,p) level of theory can be recommended for predicting rotational constants to guide the microwave spectral assignment of dimethylfluorobenzenes in particular and toluene derivatives in general.

Approaching the free rotor limit: extremely low methyl torsional barrier observed in the microwave spectrum of 2,4-dimethylfluorobenzene.

The microwave spectrum of 2,4-dimethylfluorobenzene was recorded using a molecular jet Fourier transform microwave spectrometer in the frequency range from 2.0 to 26.5 GHz. The spectral assignment and modeling were challenging due to the large tunnelling splittings resulting from the very low barrier to internal rotation of the p-methyl group that approaches the free rotor limit. Internal rotation splittings arising from two inequivalent o- and p-methyl groups were observed, analysed and modelled using the modified version of the XIAM code and the BELGI-Cs-2Tops code, giving a root-mean-square deviation of 549.1 kHz and 4.5 kHz, respectively, for a data set of 885 rotational lines. The torsional barriers of the o- and p-methyl groups were determined to be 227.039(51) cm-1 and 3.23(40) cm-1, respectively. The V3 barrier observed for the p-methyl group is lower than in any other para-methyl substituted toluene derivatives with coupled internal rotations, becoming the lowest value ever observed to date. The barrier to internal rotation of the o-methyl group next to a fluorine atom is consistently around 220 cm-1, as confirmed by comparing it to barriers observed in other toluene derivatives. The experimental rotational constants were compared to those obtained by quantum chemical calculations.

Theoretical structural and spectroscopic characterization of peroxyacetic acid (CH3-CO-OOH): study of the far infrared region.

Peroxyacetic acid, a non-rigid oxygenated organic molecule which acts in the atmosphere as a reservoir of HOX and ROX radicals, is studied using highly correlated ab initio methods with the aim of its spectroscopic characterization in the gas phase. The study focuses on the far infrared region providing reliable rovibrational parameters such as energy levels and splittings. The molecule presents three conformers that inter-convert by internal rotation, drawing a potential energy surface of 12 minima. One of them shows prominent stability due to the formation of one weak intramolecular bond between the hydrogen atom of the hydroperoxy group and the oxygen atom of the carbonyl group. For the three minimum energy structures, rotational constants and centrifugal distortion constants are provided. It may be expected that the most stable conformer is the only one contributing to the spectral features in further measurements at low temperature. In this structure, the methyl torsional barrier has been found to be very low, V3 = 88.6 cm-1 producing a splitting of 2.262 cm-1 for the ground vibrational state. The study confirms that the ν20 torsional mode interacts strongly with the other two torsional modes ν19 and ν21, but slightly with the remaining vibrations. Then, a variational procedure in three dimensions allows the exploration of the low-frequency modes. The methyl torsional fundamental ν21 was found to be 49.1 cm-1 (Ai) and 33.4 cm-1 (E). The fundamentals of ν20 (C-O bond torsion) and ν19 (OH torsion) have been computed to be 216.7 cm-1 (A2) and 218.5 cm-1 (E) and 393.6 cm-1 (A2) and 394.1 cm-1. Since non-rigidity can have effects on the reactivity due to the conformer interconversion, and transitions involving low-lying levels can be observed with many spectroscopic techniques, this work can help kinetic studies and assignments of further spectroscopic studies needed for the detection in the gas phase of trace molecules.

Electron transfer rate modulation with mid-IR in butadiyne-bridged donor-bridge-acceptor compounds.

Controlling electron transfer (ET) processes in donor-bridge-acceptor (DBA) compounds by mid-IR excitation can enhance our understanding of the ET dynamics and may find practical applications in molecular sensing and molecular-scale electronics. Alkyne moieties are attractive to serve as ET bridges, as they offer the possibility of fast ET and present convenient vibrational modes to perturb the ET dynamics. Yet, these bridges introduce complexity because of the strong torsion angle dependence of the ET rates and transition dipoles among electronic states and a shallow torsion barrier. In this study, we implemented ultrafast 3-pulse laser spectroscopy to investigate how the ET from the dimethyl aniline (D) electron donor to the N-isopropyl-1,8-napthalimide (NAP) electron acceptor can be altered by exciting the CC stretching mode (νCC) of the butadiyne bridge linking the donor and acceptor. The electron transfer was initiated by electronically exciting the acceptor moiety at 400 nm, followed by vibrational excitation of the alkyne, νCC, and detecting the changes in the absorption spectrum in the visible spectral region. The experiments were performed at different delay times t1 and t2, which are the delays between UV-mid-IR and mid-IR-Vis pulses, respectively. Two sets of torsion-angle conformers were identified, one featuring a very fast mean ET time of 0.63 ps (group A) and another featuring a slower mean ET time of 4.3 ps (group B), in the absence of the mid-IR excitation. TD-DFT calculations were performed to determine key torsion angle dependent molecular parameters, including the electronic and vibrational transition dipoles, transition frequencies, and electronic couplings. To describe the 3-pulse data, we developed a kinetic model that includes a locally excited, acceptor-based S2 state, a charge separated S1 state, and their vibrationally excited counterparts, with either excited νCC (denoted as S1Atr, S1Btr, S2Atr, and S2Btr, where tr stands for the excited triplet bond, νCC) or excited daughter modes of the νCC relaxation (S1Ah, S1Bh, S2Ah, and S2Bh, where h stands for vibrationally hot species). The kinetic model was solved analytically, and the species-associated spectra (SAS) were determined numerically using a matrix approach, treating first the experiments with longer t1 delays and then using the already determined SAS for modeling the experiments with shorter t1 delays. Strong vibronic coupling of νCC and of vibrationally hot states makes the analysis complicated. Nevertheless, the SAS were identified and the ET rates of the vibrationally excited species, S2Atr, S2Btr and S2Bh, were determined. The results show that the ET rate for the S2A species is ca. 1.2-fold slower when the νCC mode is excited. The ET rate for species S2B is slower by ca. 1.3-fold if the compound is vibrationally hot and is essentially unchanged when the νCC mode is excited. The SAS determined for the tr and h species resemble the SAS for their respective precursor species in the 2-pulse transient absorption experiments, which validates the procedure used and the results.

Surprising torsional barrier reduction in the coupled methyl internal rotations of 2,3-dimethylfuran observed by microwave spectroscopy.

The microwave spectrum of 2,3-dimethylfuran was investigated using a Fourier-transform microwave spectrometer under supersonic expansion. The molecule possesses two inequivalent methyl internal rotors, causing the splitting of each rotational transition into five torsional species. A total of 337 torsional transitions were assigned and fitted in a global fit with the program XIAM, where accurate and physically meaningful geometry and internal rotation parameters could be deduced. The different torsional species were also fitted separately with the program SFLAMS to validate the assignment. Both the global fit and the separate fits achieved standard deviations close to the measurement accuracy. The barriers to internal rotation of the ortho- and meta-methyl rotors, which are in direct proximity, were determined to be 298.274(12) cm-1 and 237.6891(47) cm-1, respectively. These values are radically lower than the respective barriers of 412.9 cm-1 and 380.5 cm-1 found for the steric-free methyl groups in 2-methylfuran and 3-methylfuran. This observation appears to be driven primarily by electrostatic effects rather than being adequately accounted for by steric effects. The experiments were accompanied by quantum chemical calculations. Benchmarking the rotational constants revealed that the MP2/6-31G(d,p) level of theory might be helpful to guide the microwave spectral assignment of methylfuran derivatives.

Low Barrier Methyl Internal Rotations and 14N Quadrupole Coupling in the Microwave Spectrum of 2,4-Dimethylthiazole.

The microwave spectrum of 2,4-dimethylthiazole was recorded using a pulsed molecular jet Fourier-transform microwave spectrometer operating in the frequency range from 2.0 to 26.5 GHz. Torsional splittings into quintets were observed for all rotational transitions due to internal rotations of two inequivalent methyl groups. Hyperfine structures arising from the nuclear quadrupole coupling of the 14N nucleus were fully resolved. The microwave spectra were analyzed using the modified version of the XIAM code and the BELGI-Cs-2Tops-hyperfine code. The barriers to methyl internal rotation of the 4- and 2-methyl groups were determined to be 396.707(25) cm-1 and 19.070(58) cm-1, respectively. The very low barrier hindering the 2-methyl torsion was a challenge for the spectral analysis and modeling, and separately fitting the five torsional species together with combination difference loops was the key for a successful assignment. The methyl torsional barriers were compared with those of other thiazole derivatives, showing the influence of the methyl group position on the barrier height. The experimental results were supported by quantum chemical calculations.

Photolytic Decarbonylation of Oxalyl Diisothiocyanate in Solid Argon Matrices tosyn‐antiCarbonyl Diisothiocyanate and Its Isomerization

AbstractOxalyl diisothiocyanate, ((CO)NCS)2, has been studied in solid argon matrices at 4.2 K with the aid of infrared (IR) spectroscopy. The spectra show mainly signals attributed to the most stableanti‐anticonformer, which is corroborated by comparison to computed anharmonic fundamental IR transitions. Upon irradiation with 254 nm UV light, oxalyl diisothiocyanate eliminates carbon monoxide under formation of carbonyl diisothiocyanate, CO(NCS)2. This reaction is only slightly exothermic by 0.4 kcal mol−1at the DLPNO‐CCSD(T)/def2‐QZVPP//B3LYP‐D3/def2‐TZVPP level of theory. Remarkably, photolysis produces mostly the less stablesyn‐anticonformer of carbonyl diisothiocyanate. Subsequent annealing at 30 K for two minutes results in a structural relaxation to the 0.7 kcal mol−1more stablesyn‐synconformer confirming a low torsional barrier height between the isomers.

Phosphorus fluoride exchange: Multidimensional catalytic click chemistry from phosphorus connective hubs

Phosphorus Fluoride Exchange (PFEx) represents a cutting-edge advancement in catalytic click-reaction technology. Drawing inspiration from Nature's phosphate connectors, PFEx facilitates the reliable coupling of P(V)-F loaded hubs with aryl alcohols, alkyl alcohols, and amines to produce stable, multidimensional P(V)-O and P(V)-N linked products. The rate of P-F exchange is significantly enhanced by Lewis amine base catalysis, such as 1,5,7-triazabicyclo[4.4.0]dec-5-ene (TBD). PFEx substrates containing multiple P-F bonds are capable of selective, serial exchange reactions via judicious catalyst selection. In fewer than four synthetic steps, controlled projections can be deliberately incorporated along three of the four tetrahedral axes departing from the P(V) central hub, thus taking full advantage of the potential for generating three-dimensional diversity. Furthermore, late-stage functionalization of drugs and drug fragments can be achieved with the polyvalent PFEx hub, hexafluorocyclotriphosphazene (HFP), as has been demonstrated in prior research.

Effects of Y-nodes in DGEBA/TDE-85/MTHPA blends on their thermal and mechanical properties: MD simulation and experimental study

With the development of alternate electrical power system and the improvement of voltage level, the operation conditions faced by epoxy resin (ER) insulation materials are becoming more and more complex. The traditional ER materials have been difficult to meet the increasingly stringent requirements. In this paper, the thermal and mechanical properties of DGEBA/TDE-85/MTHPA blend system were studied by molecular dynamics (MD) simulation and experiment. The results show that the addition of TDE-85 can significantly improve the thermal and mechanical properties, and the comprehensive improvement effect is the best when the molar ratio of DGEBA and TDE-85 is about 8:2. The experimental results are consistent with the simulation results. Further analysis of the micro-parameters of the monomer and the cross-linking network found that the torsional energy barrier of TDE-85 is higher than DGEBA. And the compatibility of the two ER is better when the ratio is 8:2. In addition, TDE-85 can introduce high-stability Y-nodes into the system, making the cross-linked network more stable, which has a significant effect on improving the thermal and mechanical properties. The research provide a reference for the blending modification of high-performance ER for high-voltage insulation.

Torsional Rotation in Ditopic Receptor Host and its Complex Formation with Resorcinol Guest: A Computational Study.

Noncovalent interactions due to the presence of heteroatoms in supramolecular compounds have gained a lot of attention. These different heteroatom-based supramolecular compounds have inspired us to examine the noncovalent interaction in the isolated host and host-guest complexes. In view of this, in the current manuscript, we investigated the stability and torsional energy barrier of different conformers of the ditopic receptor host 1,6-bis(2,6-bis(benzothiazol-2-yl) pyridine-4-yloxy) hexane (bbh). The conformer that is accompanied by intramolecular C-H⋯N and C-H⋯S interactions is relatively more stable than the others. Due to torsional angle rotation within the host, the C-H⋯N and C-H⋯S interactions get disrupted and exhibit different binding sites for capturing guest molecules. In addition, we have extended the investigation to understand the interaction energy and nature of interaction in host-guest (1 : 1 and 1 : 2) complexes formed between the host (bbh) and guest (resorcinol) by using different DFT functionals. Extended transition state-natural orbital chemical valence (ETS-NOCV) analysis of complexes revealed that the electrostatic interaction significantly contributes to the host-guest interaction energy. The noncovalent (NCI) analysis provides the existence of intermolecular hydrogen bonding and other weak interactions within the complexes.

Towards practical and massively parallel quantum computing emulation for quantum chemistry

Quantum computing is moving beyond its early stage and seeking for commercial applications in chemical and biomedical sciences. In the current noisy intermediate-scale quantum computing era, the quantum resource is too scarce to support these explorations. Therefore, it is valuable to emulate quantum computing on classical computers for developing quantum algorithms and validating quantum hardware. However, existing simulators mostly suffer from the memory bottleneck so developing the approaches for large-scale quantum chemistry calculations remains challenging. Here we demonstrate a high-performance and massively parallel variational quantum eigensolver (VQE) simulator based on matrix product states, combined with embedding theory for solving large-scale quantum computing emulation for quantum chemistry on HPC platforms. We apply this method to study the torsional barrier of ethane and the quantification of the protein–ligand interactions. Our largest simulation reaches 1000 qubits, and a performance of 216.9 PFLOP/s is achieved on a new Sunway supercomputer, which sets the state-of-the-art for quantum computing emulation for quantum chemistry.

The mismatch repair endonuclease MutLα tethers duplex regions of DNA together and relieves DNA torsional tension.

In eukaryotic mismatch repair, MutS homologs recognize mismatches and recruit the MutLα endonuclease which introduces a nick in the newly replicated, error-containing DNA strand. The nick occurs in response to the mismatch, but at a site up to several hundred base pairs away. The MutLα nick promotes mismatch excision by an exonuclease (Exo1) or removal by the strand displacement activity of a DNA polymerase which may work in conjunction with a flap endonuclease. Models have suggested that MutL homolog endonucleases form oligomeric complexes which facilitate and are activated by strand capture mechanisms, although such models have never been explicitly tested. We present evidence that the mismatch repair MutLα endonuclease is activated by DNA-DNA associations and that it can use this property to overcome DNA torsional barriers. Using DNA ligation and pull-down experiments, we determined that the MutLα endonuclease associates two DNA duplexes. Using nuclease assays, we determined that this activity stimulates MutLα's endonuclease function. We also observe that MutLα enhances a topoisomerase without nicking the DNA itself. Our data provide a mechanistic explanation for how MutL proteins interact with DNA during mismatch repair, and how MutL homologs participate in other processes, such as recombination and trinucleotide repeat expansions.