As optical properties, the ultraviolet-visible (UV-Vis) absorption spectra of capsanthin-based red natural dye are a decisive parameter for their usage in various applications. Thus, accurately predicting the maximum UV-Vis wavelength ( λmax ) values is critical in designing dye-conjugated material. Extensive metadynamics simulations were carried out to generate capsanthin conformers at various levels of the extended tight-binding method. Benchmarking the time-dependent density-functional theory (TD-DFT) methods help understand the results of a particular functional and allows a comparison between results obtained with different functional. The long-range correction (LC) scheme in LC-TD-DFT-D4/ωB97X/def2-SVP has been found to reproduce the experimental λmax,  and exhibited the effect of conformational changes to the calculated wavelengths. On the other hand, an inexpensive yet efficient LC-TD-DFTB method reproduced the experimental λmax insensitive to conformational changes.

Here, we present a parametrization of the metadynamics simulations for reactions involving breaking the chemical bonds along a single collective variable coordinate. The parameterization is based on the similarity between the bias potential in metadynamics and the quantum potential in the de Broglie-Bohm formalism. We derive the method and test it on two prototypical reaction types: proton transfer and breaking of the cyclohexene cycle (reversed Diels-Alder reaction).

This study is carried out using the COGITO force field to determine whether the thermodynamic melting point of pure triacylglyceride crystals can be predicted using molecular dynamics simulations. The triacylglycerides used in this study are both saturated and unsaturated, as well as symmetrical and asymmetrical, to test the robustness of both the force field and the direct heating methodology described in this paper. Given the nonequilibrium nature of a melting system, a larger number of simulations are required to ensure that the results are sufficiently converged, that is, with little fluctuation and a small confidence interval. The study also highlights the importance of the presence of defects, in this case as voids, to lower the melting nucleation energy barrier of the crystals and avoid superheating of the systems being tested. The size of these defects is much larger than what would be found in a physical crystal, however, the simple and robust procedure that was developed allows the accurate prediction of melting points of the different triacylglycerides.

A nonionizing ultrafast laser pulse of 20-fs duration with a peak amplitude electric-field ±E = 200 × 10-4 a.u. was simulated. It was applied to the ethene molecule to consider its effect on the electron dynamics, both during the application of the laser pulse and for up to 100 fs after the pulse was switched off. Four laser pulse frequencies ω = 0.2692, 0.2808, 0.2830, and 0.2900 a.u. were chosen to correspond to excitation energies mid-way between the (S1 ,S2 ), (S2 ,S3 ), (S3 ,S4 ) and (S4 ,S5 ) electronic states, respectively. Scalar quantum theory of atoms in molecules (QTAIM) was used to quantify the shifts of the C1C2 bond critical points (BCPs). Depending on the frequencies ω selected, the C1C2 BCP shifts were up to 5.8 times higher after the pulse was switched off compared with a static E-field with the same magnitude. Next generation QTAIM (NG-QTAIM) was used to visualize and quantify the directional chemical character. In particular, polarization effects and bond strengths, in the form of bond-rigidity vs. bond-flexibility, were found, for some laser pulse frequencies, to increase after the laser pulse was switched off. Our analysis demonstrates that NG-QTAIM, in partnership with ultrafast laser irradiation, is useful as a tool in the emerging field of ultrafast electron dynamics, which will be essential for the design, and control of molecular electronic devices.

Theoretical predictions and recent experimental studies lead to the discovery of an exciting new member of the carbon allotrope family polyynic cyclo[18]carbon (C18 ). Present investigation aims to probe the structure, stability, and properties of coinage metal (M)@C18 complexes using density functional theory (DFT) calculations. The DFT results unequivocally show that even Cu@C18 , Ag@C18 , and Au@C18 complexes substantially preserve the ground state polyynic structure of C18 . It is also worth to mention that only Au@C18 is a stable D9h structure, however the symmetry is distorted in the case of Cu@C18 and Ag@C18 . Due to computational limitations, in this investigation the M@C18 complexes were scrutinized using the C2v sub abelian group of D9h . The highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) of D9h conformers are a singlet a1 and two same value singlets a1  ⊕ b1 generated from doublet e, respectively. The non-covalent interaction index (NCI), quantum theory of atoms in molecule (QTAIM), and energy decomposition analysis (EDA) vividly explains the interaction between a coinage metal atom and C18 ring. It is found from the results that the stability of Cu@C18 Ag@C18 , and Au@C18 is governed by the attractive electrostatic, orbital and dispersion interaction.

The recent discovery that anaerobic methanogens can reductively dissolve pyrite and utilize dissolution products as a source of iron and sulfur to meet their biosynthetic demands for these elements prompted the development of atomic-scale nanoparticle models, as maquettes of reactive surface sites, for describing the fundamental redox steps that take place at the mineral surface during reduction. The given report describes our computational approach for modeling n(FeS2 ) nanoparticles originated from mineral bulk structure. These maquettes contain a comprehensive set of coordinatively unsaturated Fe(II) sites that are connected via a range of persulfide (S2 2- ) ligation. In addition to the specific maquettes with n = 8, 18, and 32 FeS2 units, we established guidelines for obtaining low-energy structures by considering the pattern of ionic, covalent, and magnetic interactions among the metal and ligand sites. The developed models serve as computational nano-reactors that can be used to describe the reductive dissolution mechanism of pyrite to better understand the reactive sites on the mineral, where microbial extracellular electron-transfer reactions can occur.

SARS-CoV-2 cysteine proteases are essential nonstructural proteins due to their role in the formation of the virus multiple enzyme replication-transcription complex. As a result, those functional proteins are extremely relevant targets in the development of a new drug candidate to fight COVID-19. Based on this fact and guided by the bioisosterism strategy, the present work has selected 126 out of 1050 ligands from DrugBank website. Subsequently, 831 chemical analogs containing bioisosteres, some of which became structurally simplified, were created using the MB-Isoster software, and molecular docking simulations were performed using AutoDock Vina. Finally, a study of physicochemical properties, along with pharmacokinetic profiles, was carried out through SwissADME and ADMETlab 2.0 platforms. The promising results obtained with the molecules encoded as DB00549_BI_005, DB04868_BI_003, DB11984_BI_002, DB12364_BI_006 and DB12805_BI_004 must be confirmed by molecular dynamics studies, followed by in vitro and in vivo empirical tests that ratify the advocated in-silico results.

With the rise of quantum mechanical/molecular mechanical (QM/MM) methods, the interest in the calculation of molecular assemblies has increased considerably. The structures and dynamics of such assemblies are usually governed to a large extend by intermolecular interactions. As a result, the corresponding potential energy surfaces are topological rich and possess many shallow minima. Therefore, local structure optimizations of QM/MM molecular assemblies can be challenging, in particular if optimization constraints are imposed. To overcome this problem, structure optimization in normal coordinate space is advocated. To do so, the external degrees of freedom of a molecule are separated from the internal ones by a projector matrix in the space of the Cartesian coordinates. Here we extend this approach to Cartesian constraints. To this end, we devise an algorithm that adds the Cartesian constraints directly to the projector matrix and in this way eliminates them from the reduced coordinate space in which the molecule is optimized. To analyze the performance and stability of the constrained optimization algorithm in normal coordinate space, we present constrained minimizations of small molecular systems and amino acids in gas phase as well as water employing QM/MM constrained optimizations. All calculations are performed in the framework of auxiliary density functional theory as implemented in the program deMon2k.

In local hybrid functionals (LHs), a local mixing function (LMF) determines the position-dependent exact-exchange admixture. We report new LHs that focus on an improvement of the LMF in the core region while retaining or partly improving upon the high accuracy in the valence region exhibited by the LH20t functional. The suggested new pt-LMFs are based on a Padé form and modify the previously used ratio between von Weizsäcker and Kohn-Sham local kinetic energies by different powers of the density to enable flexibly improved approximations to the correct high-density and iso-orbital limits relevant for the innermost core region. Using TDDFT calculations for a set of K-shell core excitations of second- and third-period systems including accurate state-of-the-art relativistic orbital corrections, the core part of the LMF is optimized, while the valence part is optimized as previously reported for test sets of atomization energies and reaction barriers (Haasler et al., J Chem Theory Comput 2020, 16, 5645). The LHs are completed by a calibration function that minimizes spurious nondynamical correlation effects caused by the gauge ambiguities of exchange-energy densities, as well as by B95c meta-GGA correlation. The resulting LH23pt functional relates to the previous LH20t functional but specifically improves upon the core region.

The alternant polycyclic aromatic hydrocarbon pyrene has photophysical properties that can be tuned with different donor and acceptor substituents. Recently, a D (donor)-Pyrene (bridge)-A (acceptor) system, DPA, with the electron donor N,N-dimethylaniline (DMA), and the electron acceptor trifluoromethylphenyl (TFM), was investigated by means of time-resolved spectroscopic measurements (J. Phys. Chem. Lett. 2021, 12, 2226-2231). DPA shows great promise for potential applications in organic electronic devices. In this work, we used the ab initio second-order algebraic diagrammatic construction method ADC(2) to investigate the excited-state properties of a series of analogous DPA systems, including the originally synthesized DPAs. The additionally investigated substituents were amino, fluorine, and methoxy as donors and nitrile and nitro groups as acceptors. The focus of this work was on characterizing the lowest excited singlet states regarding charge transfer (CT) and local excitation (LE) characters. For the DMA-pyrene-TFM system, the ADC(2) calculations show two initial electronic states relevant for interpreting the photodynamics. The bright S1 state is locally excited within the pyrene moiety, and an S2 state is localized ~0.5 eV above S1 and characterized as a donor to pyrene CT state. HOMO and LUMO energies were employed to assess the efficiency of the DPA compounds for organic photovoltaics (OPVs). HOMO-LUMO and optical gaps were used to estimate power conversion and light-harvesting efficiencies for practical applications in organic solar cells. Considering the systems using smaller D/A substituents, compounds with the strong acceptor NO2 substituent group show enhanced CT and promising properties for use in OPVs. Some of the other compounds with small substituents are also found to be competitive in this regard.

We studied the structural, electronic, phonon spectrum and thermoelectric properties of ternary LuMSb (M = Ni, Pd, Pt) half Heusler compounds by using first principles method. The electronic properties are calculated via energy band structure and density of states by using GGA + U approximation. The calculations reveal that the replacement of Ni with Pd and Pt, energy gap decreases and LuNiSb, LuPdSb are found to have narrow indirect band gaps and exhibit semiconducting nature, while LuPtSb is found to be a gapless semiconductor. Phonon band structure calculations give only positive values of phonon frequency indicating the dynamically stability of these compounds. The thermoelectric properties have been computed using semi-classical Boltzmann transport theory. We found high Seebeck coefficient (S) and high power factor (PF) for LuNiSb and LuPdSb compounds in the whole temperature range. The ZT values of LuNiSb and LuPdSb are high in general and reach a maximum of 0.67 and 0.69 at 450 K, respectively, whereas 0.39 is the maximum ZT value for LuPtSb at the same temperature. These findings propose LuNiSb and LuPdSb compounds as promising materials for thermoelectric applications at room temperature.

Time-dependent density functional theory (TDDFT) was applied to gain insights into the electronic and vibrational spectroscopic properties of an important electron transport mediator, methyl viologen (MV2+ ). An organic dication, MV2+ has numerous applications in electrochemistry that include energy conversion and storage, environmental remediation, and chemical sensing and electrosynthesis. MV2+ is easily reduced by a single electron transfer to form a radical cation species (MV•+ ), which has an intense UV-visible absorption near 600 nm. The redox properties of the MV2+ /MV•+ couple and light-sensitivity of MV•+ have made the system appealing for photo-electrochemical energy conversion (e.g., solar hydrogen generation from water) and the study of photo-induced charge transfer processes through electronic absorption and resonance Raman spectroscopic measurements. The reported work applies leading TDDFT approaches to investigate the electronic and vibrational spectroscopic properties of MV2+ and MV•+ . Using a conventional hybrid exchange functional (B3-LYP) and a long-range corrected hybrid exchange functional (ωB97X-D3), including with a conductor-like polarizable continuum model to account for solvation, the electronic absorption and resonance Raman spectra predicted are in good agreement with experiment. Also analyzed are the charge transfer character and natural transition orbitals derived from the TDDFT vertical excitations calculated. The findings and models developed further the understanding of the electronic properties of viologens and related organic redox mediators important in renewable energy applications and serve as a reference for guiding the interpretation of electronic absorption and Raman spectra of the ions.

In this study, we present the results of a search for new stable structures of SrC 2 O 5 and BaC 2 O 5 in the pressure range of 0-100 GPa based on the density functional theory and crystal structure prediction approaches. We have shown that the recently synthesized pyrocarbonate structure SrC 2 O 5 - P21/c is thermodynamically stable for both SrC 2 O 5 and BaC 2 O 5 . Thus, SrC 2 O 5 - P21/c is stable relative to decomposition reaction above 10 GPa, while the lower-pressure stability limit for BaC 2 O 5 - P21/c is 5 GPa, which is the lowest value for the formation of pyrocarbonates. For SrC 2 O 5 , the following polymorphic transitions were found with increasing pressure: P21/c → Fdd2 at 40 GPa and 1000 K, Fdd2 → C2 at 90 GPa and 1000 K. SrC 2 O 5 - Fdd2 and SrC 2 O 5 - C2 are characterized by the framework and layered structures of [CO 4 ] 4- tetrahedra, respectively. For BaC 2 O 5 , with increasing pressure, decomposition of BaC 2 O 5 - P21/c into BaCO 3 and CO 2 is observed at 34 GPa without any polymorphic transitions.

Relativistic adapted Gaussian basis sets of small and medium sizes are presented in this study for all elements from cesium to radon, including some alternative electron configurations. Both basis sets are made free of variational prolapse, being developed by means of a polynomial version of the generator coordinate Dirac-Fock method. In addition, these sets were designed to be promptly used with two popular finite nuclear models, uniform sphere and Gaussian nuclei. The largest basis set errors found with the uniform sphere nucleus are 27.3 and 10.6 mHartree, respectively, for the small- and medium-size sets. The largest basis set errors obtained with the Gaussian nuclear model are smaller, reaching 23.2 and 7.1 mHartree for the small- and medium-size sets, respectively. Soon, these basis sets will be augmented with polarization functions to be properly used in molecular calculations.

Molecular dynamics simulations were performed to study structural and dynamic properties of polar butanamine/water/butanamine, pentanoic acid/water/pentanoic acid, butanethiol/water/butanethiol, and nonpolar pentane/water/pentane systems. The mass density profiles along the interface normal to the organic liquid/water system, the difference in the local structure of H 2 O molecules in bulk and in the vicinity of interface, as well as the diffusion behavior of water molecules at the interface with above-mentioned organic liquids have been investigated. Our MD simulation has shown that the diffusion of water molecules across the water/organic liquid interface is influenced by the hydrogen bonds nHB between water molecules and the terminal groups of organic liquids. It was found that the loss of the hydrogen bonds nHB in the nonpolar organic liquid leads to a decrease in the value of the normal component of the diffusion coefficient Dz , while the tangential diffusion coefficients, both Dx and Dy , increase.

The double perovskites are become the emerging aspirant to fulfill the demand of energy. Therefore, the optoelectronic, elastic and transport characteristics of Ba2 XMoO6 (X = Zn, Cd) are addressed systemically. The elastic constants show the mechanical stability. The nature of Ba2 ZnMoO6 is brittle and Ba2 CdMoO6 is ductile with large values of Debye temperature covalent bonding. The electronic band structures exhibit band gaps of 2.81 and 2.98 eV, which increase their importance for optoelectronic applications. The absorption of light energy, optical loss, refractive index, polarization of light energy are addressed in the energy range zero to 14 eV. Furthermore, thermoelectric characteristics are computed against chemical potentials at 300, 600, and 900 K. The chemical potential decides the p-type nature, with holes as majority carriers. The increasing temperature increases the power factor and figure of merit. Therefore, the optoelectronic and thermoelectric characteristics reveals the importance of studied DPs for energy applications.

This work reports on a spin-pure configuration-based implementation of the heatbath configuration interaction (HCI) algorithm for selective configuration interaction. Besides the obvious advantage of being spin-pure, the presented method combines the compactness of the configurational ansatz with the known efficiency of the HCI algorithm and a variety of algorithmic and conceptual ideas to achieve a high level of performance. In particular, through pruning of the selected configurational space after HCI selection by means of a more strict criterion, a more compact wavefunction representation is obtained. Moreover, the underlying logic of the method allows us to minimize the number of redundant matrix-matrix multiplications while making use of just-in-time compilation to achieve fast diagonalization of the Hamiltonian. The critical search for 2-electron connections within the configurational space is facilitated by a tree-based representation thereof as suggested previously by Gopal et al. Usage of a prefix-based parallelization and batching during the calculation of the PT2-correction leads to a good load balancing and significantly reduced memory requirements for these critical steps of the calculation. In this way, the need for a semistochastic approach to the PT2 correction is avoided even for large configurational spaces. Finally, several test-cases are discussed to demonstrate the strengths and weaknesses of the presented method.

Conformational space annealing (CSA), a global optimization method, has been applied to various protein structure modeling tasks. In this paper, we applied CSA to the cryo-EM structure modeling task by combining the python subroutine of CSA (PyCSA) and the fast relax (FastRelax) protocol of PyRosetta. Refinement of initial structures generated from two methods, rigid fitting of predicted structures to the Cryo-EM map and de novo protein modeling by tracing the Cryo-EM map, was performed by CSA. In the refinement of the rigid-fitted structures, the final models showed that CSA can generate reliable atomic structures of proteins, even when large movements of protein domains were required. In the de novo modeling case, although the overall structural qualities of the final models were rather dependent on the initial models, the final models generated by CSA showed improved MolProbity scores and cross-correlation coefficients to the maps. These results suggest that CSA can accomplish flexible fitting and refinement together by sampling diverse conformations effectively and thus can be utilized for cryo-EM structure modeling.

The double proton transfer (PT) reaction has been investigated in the [2,2'-bipyridyl]-3-3'-diol, a complex molecule where the proton movements is coupled to significant rearrangement of the electronic structure. Moreover, the reaction could be concerted, that is the two protons are exchanged simultaneously, or stepwise, where the two protons are transferred sequentially. To this end, a static exploration of the potential energy surface (PES) was carried together with the analysis of the free-energy surface (FES), both surfaces being evaluated at density functional theory level and different exchange-correlation functionals. While the concerted mechanism has been clearly discharged, the characteristics of the stepwise PT significantly depends on the chosen functionals, some suggesting a clear stepwise mechanism characterized by a stable reaction intermediates and two transitions states, whereas other approaches propend for a asynchronous PT, with a single TS. These features appear on both PES and FES, albeit some differences appears due to their different nature.

FSATOOL is an integrated molecular simulation and data analysis program. Its old molecular dynamics engine only supports simulations in vacuum or implicit solvent. In this work, we implement the well-known smooth particle mesh Ewald method for simulations in explicit solvent. The new developed engine is runnable on both CPU and GPU. All the existed analysis modules in the program are compatible with the new engine. Moreover, we also build a complete deep learning module in FSATOOL. Based on the module, we further implement two useful trajectory analysis methods: state-free reversible VAMPnets and time-lagged autoencoder. They are good at searching the collective variables related to the conformational transitions of biomolecules. In FSATOOL, these collective variables can be further used to construct a bias potential for the enhanced sampling purpose. We introduce the implementation details of the methods and present their actual performances in FSATOOL by a few enhanced sampling simulations.

Discovery of target-binding molecules, such as aptamers and peptides, is usually performed with the use of high-throughput experimental screening methods. These methods typically generate large datasets of sequences of target-binding molecules, which can be enriched with high affinity binders. However, the identification of the highest affinity binders from these large datasets often requires additional low-throughput experiments or other approaches. Bioinformatics-based analyses could be helpful to better understand these large datasets and identify the parts of the sequence space enriched with high affinity binders. BinderSpace is an open-source Python package that performs motif analysis, sequence space visualization, clustering analyses, and sequence extraction from clusters of interest. The motif analysis, resulting in text-based and visual output of motifs, can also provide heat maps of previously measured user-defined functional properties for all the motif-containing molecules. Users can also run principal component analysis (PCA) and t-distributed stochastic neighbor embedding (t-SNE) analyses on whole datasets and on motif-related subsets of the data. Functionally important sequences can also be highlighted in the resulting PCA and t-SNE maps. If points (sequences) in two-dimensional maps in PCA or t-SNE space form clusters, users can perform clustering analyses on their data, and extract sequences from clusters of interest. We demonstrate the use of BinderSpace on a dataset of oligonucleotides binding to single-wall carbon nanotubes in the presence and absence of a bioanalyte, and on a dataset of cyclic peptidomimetics binding to bovine carbonic anhydrase protein. BinderSpace is openly accessible to the public via the GitHub website: https://github.com/vukoviclab/BinderSpace.

The experimental gas-phase thermochemistry of reactions: M+ (S)n-1  + S → M+ (S)n and M+ + nS→ M+ (S)n , where M is an alkali metal and S is acetonitrile/ammonia, is reproduced. Three approximations are tested: (1) scaled rigid-rotor-harmonic-oscillator (sRRHO); (2) the sRRHO(100) identical to (1), but with all vibrational frequencies smaller than 100 cm-1 replaced with 100 cm-1 ; (3) Grimme's modified scaled RRHO (msRRHO) (Grimme, Chem. Eur. J., 2012, 18, 9955-9964). The msRRHO approach provides the most accurate reaction entropies with the mean unsigned error (MUE) below 5.5 cal mol-1  K-1 followed by sRRHO(100) and sRRHO with MUEs of 7.2 and 16.9 cal mol-1  K-1 . For the first time, we propose using the msRRHO scheme to calculate the enthalpy contribution that is further utilized to arrive at reaction Gibbs free energies (∆Gr ) ensuring the internal consistency. The final ∆Gr MUEs for msRRHO, sRRHO(100) and sRRHO schemes are 1.2, 3.6 and 3.1 kcal mol-1 .

We introduce a fermionic potential, vf , as a comprehensive measure of electron (de)localization in atomic-molecular systems. Unlike other common descriptors as ELF, LOL, etc., it characterizes all physical effects responsible for (de)localization of electrons, namely: an exchange hole depth, its tendency to change, a sensitivity of an exchange correlation hidden in a pair density and kinetic potential to local variations in electron density. Wells in the vf distribution correspond to the domains of maximum electron localization, while the potential's barriers prevent delocalization of electrons through them. It also estimates bond orders and successfully reveals the impact of chemical modifications or environmental effects on the delocalization of electrons in molecules and crystals. The vf components provide a unique opportunity to compare the influence of the mentioned physical effects on electron (de)localization. This merges physical and chemical views of electron delocalization using functions appearing in density functional theory.

Fragmentation-based methods for nuclear magnetic resonance (NMR) chemical shift calculations have become more and more popular in first-principles calculations of large molecules. However, there are many options for a fragmentation-based method to select, such as theoretical methods, fragmentation schemes, the number of levels of theory, etc. It is important to study the optimal combination of the options to achieve a good balance between accuracy and efficiency. Here we investigate different combinations of options used by a fragmentation-based method, the eXtended ONIOM (XO) method, for 13 C chemical shift calculations on a set of organic and biological molecules. We found that: (1) introducing Hartree-Fock exchange into density functional theory (DFT) could reduce the calculation error due to fragmentation in contrast to pure DFT functionals, while a hybrid functional, xOPBE, is generally recommended; (2) fragmentation schemes generated from the molecular tailoring approach (MTA) with small level parameter n, for example, n = 2 and the degree-based fragmentation method (DBFM) with n = 1, are sufficient to achieve satisfactory accuracy; (3) the two-level XO (XO2) NMR calculation is superior to the calculation with only one level of theory, as the second level (i.e., low level) of theory provides a way to well describe the long-range effect. These findings are beneficial to practical applications of fragmentation-based methods for NMR chemical shift calculations of large molecules.