Psi4 1.1: An Open-Source Electronic Structure Program Emphasizing Automation, Advanced Libraries, and Interoperability

Unprecedented binding of Thioflavin T with well-ordered spherical aggregates: A false positive?

Amyloidogenic protein aggregation is a hallmark of numerous neurodegenerative diseases, including Alzheimer's and Parkinson's diseases. Thioflavin T (ThT), which selectively interacts with fibrillar amyloid structures, holds significant promise for diagnostic and therapeutic applications. Herein, we investigate the binding behaviour of Thioflavin T (ThT), a widely employed amyloid-specific fluorophore, with well-ordered spherical aggregates formed by dipeptides Boc-Phe-Trp-OMe (FW), Boc-Val-Trp-OMe (VW), Boc-Leu-Trp-OMe (LW) and Boc-Ile-Trp-OMe (IW). Our findings indicate that despite their non-amyloid nature, the well-ordered spherical dipeptide aggregates effectively sequester ThT molecules, enhancing fluorescence. The binding of ThT molecules to the dipeptides was further confirmed by fluorescence microscopy, which produced beautiful bright green-fluorescent images from the spherical structures and also with DFT studies. The apparent binding constant calculation suggests a reasonably good binding affinity between ThT and the designed dipeptide molecules, and the thermodynamic parameters analysis indicates the spontaneity of the binding process during complexation. The spherical nature of the dipeptides was confirmed by FESEM and FETEM. Circular Dichroism (CD) and Solid-state FTIR studies suggest that the dipeptides in solution coexist in multiple conformations. This study underscores the universality of ThT as a probe for fibrillar aggregate, sheds light on the broader implications of molecular recognition, and highlights the importance of investigating unexpected interactions in supramolecular chemistry and peptide-based materials. This is the first report of a ThT-stained spherical supramolecular structure made up of standard amino acids.

Quantifying the Cooperativity of Backbone Hydrogen Bonding

The hydrogen bonds (H-bonds) between backbone amide and carbonyl groups are fundamental to the stability, structure, and dynamics of proteins. A key feature of such hydrogen bonding interactions is that multiple H-bonds can enhance each other when aligned, as such in theα $$ \alpha $$ -helix orβ $$ \beta $$ -sheet secondary structures. To better understand this cooperative effect, we propose a new physical quantity to evaluate the cooperativity of intermolecular interactions. Using H-bond aligned N-methylacetamide molecules as the model system, we assess the cooperativity of protein backbone hydrogen bonds using quantum chemistry (QM) calculations at the MP2/aug-cc-pVTZ level, revealing cooperative energies ranging from 2 to 4.3 kcal/mol. A set of protein force fields was benchmarked against QM results. While the additive force field failed to reproduce cooperativity, polarizable force fields, including the Drude and AMOEBA protein force fields, have been found to reproduce the trend of QM results, albeit with smaller magnitude. This work demonstrates the theoretical utility of the proposed formula for quantifying cooperativity and its relevance in force field parameterization. Incorporating cooperative energy into polarizable models presents a pathway to achieving more accurate simulations of biomolecular systems.

Non-Covalent Molecular Interaction Rules to Define Internal Dimer Coordinates for Quantum Mechanical Potential Energy Scans

Non-covalent interactions (NCI) dominate the properties of condensed phase systems. Towards a detailed understanding of NCI, quantum mechanical (QM) methods allow for accurate estimates of interaction energies and geometries, allowing for the contributions of different types of NCI to condensed phase properties to be understood. In addition, such information can be used for the optimization of empirical force fields, including the specific contribution of electrostatic versus van der Waals interactions. However, to date, the relative orientation of monomers defining molecular interactions of dimers is often based on full geometry optimizations of all degrees of freedom or extracted from known experimental structures of biological molecules. In such cases, the spatial relationship of the monomers often leads to multiple atoms in each monomer making significant contributions to the interactions occurring in the dimer, confounding understanding of the contributions of specific atoms or functional groups. To overcome this, a workflow is presented that allows for systematic control of the interaction orientation between monomers to be performed through the use of molecular interaction rules (MIR) in an extendable tool that can be applied to a broad range of chemical space. Using the "MIR workflow" allows a user to perform automation of the determination of well-defined monomer interaction orientations in dimers using Z-matrices, allowing for potential energy scans (PES) to be performed on combinatorial pairs of the monomers. In addition, compiled monomer and dimer geometries and PES data are stored in an extendable database. Illustration of the utility of the workflow is performed based on a collection of 89 monomers encompassing a variety of functional group classes from which 10,616 interaction dimers can be automatically generated. PES between all dimers were calculated at the QM HF/6-31G*, MP2/6-31G*, and ωb97x-d3/6-31G* model chemistries. In addition, analysis of the benzene dimer in three interaction orientations, a hydrogen bond interaction between azetidinone and N-methylacetamide, and the interaction of pyridine with acetone in the Burgi-Dunitz orientation are presented including results with the aug-cc-pVDZ basis set. Results show the impact of different QM model chemistries on minimum interaction energies and distances over a large ensemble of intermolecular interactions with emphasis on the contributions of dispersion.

Ng@M10H10: nobel gas trapping by an alkali hydride cage

The stability of noble gas encapsulated M10H10 (M = Li, Na, K) cage structures is examined using density functional and ab initio molecular dynamics simulations. To ascertain the effectiveness of M10H10 cages in encapsulating noble gas atoms, dissociation energy and dissociation enthalpy are computed. Ab initio molecular dynamics simulation shows that the systems are kinetically stable and maintain their structures over the simulation time (500 fs) at three different temperatures (300 K, 150 K, and 77 K), despite the fact that they are thermodynamically less stable or metastable with regard to the dissociation of individual Ng atoms and parent cages. The non-covalent nature of the Ng-Ng (Ng = He, Ne, Ar) interactions in Ng2@K10H10 are demonstrated by electron density analysis. In every cage system, the Ng-H bonds are also found to be non-covalent in nature.

Exploring Secondary Electrostatic Interactions Using Molecular Rotors: Implications for SN2 Reactions

Benzylic and allylic electrophiles are well known to react faster in SN2 reactions than aliphatic electrophiles, but the origins of this enhanced reactivity are still being debated. Galabov, Wu, and Allen recently proposed that electrostatic interactions in the transition state between the nucleophile (Nu) and the sp2 carbon (C2) adjacent to the electrophilic carbon (C1) play a key role. To test this secondary electrostatic hypothesis, molecular rotors were designed that form similar through-space electrostatic interactions with C2 in their bond rotation transition states without forming bonds to C1. This largely eliminates the alternative explanation of stabilizing conjugation effects between C1 and C2 in the transition state. The rotor barriers were strongly correlated with the experimentally measured SN2 free energy. Notably, rotors where C2 was sp2 or sp-hybridized had barriers that were consistently 0.5-2.0 kcal mol-1 lower than those for rotors where C2 was sp3-hybridized. Computational studies of atomic charges were consistent with the formation of stabilizing secondary electrostatic interactions. Further confirmation came from observing the benzylic effect in rotors where the first atom was varied, including oxygen, sulfur, nitrogen, and sp2-carbon. In summary, these studies provided strong experimental support for the role of secondary electrostatic interactions in the SN2 reaction.

Predicting the Brain-To-Plasma Unbound Partition Coefficient of Compounds via Formula-Guided Network

Blood-brain barrier (BBB) permeability plays a crucial role in determining drug efficacy in the brain, with the brain-to-plasma unbound partition coefficient (Kp,uu) recognized as a key parameter of BBB permeability in drug development. However, Kp,uu data are scarce and mostly in-house. In predicting Kp,uu the generality and applicability of existing empirical scoring models remain underexplored. To address this, we established a public rat Kp,uu data set through data mining and developed a formula-guided deep learning model, CMD-FGKpuu, which performed well on multiple benchmark tests, marking good demonstration of the potential of deep learning for Kp,uu prediction. Additionally, the model can be fine-tuning with project-specific experimental data, thus improving its practical utility. The findings offer an effective tool for predicting BBB permeability in drug development and introduce a new perspective for applying few-shot learning in the pharmaceutical field.

Weak Interactions Break Strong Bonds: Noncovalent Complexes of H-X with N-Heterocycles

The phenomenon of positive cooperativity in noncovalent complexes, arising from electron donor-acceptor (eDA) interactions and subsequent electron reorganization, has been investigated by using density functional theory (DFT) at the ωB97XD/6-311 + G(3df,2pd) level. The study focuses on the interaction of various nitrogen- and oxygen-containing heterocycles with HF and HCl molecules. The formation of dimer complexes leads to electron flow from the nitrogen lone pair to the hydrogen halide, enhancing the electron density on the halogen atom, as made evident by molecular electrostatic potential (MESP) analysis. The introduction of additional HX molecules induces positive cooperativity, strengthening noncovalent N···H interaction and ultimately facilitating spontaneous H-X bond cleavage and formation of stable ion pairs. Substituent effects and positional isomerism in substituted pyridines reveal that electron-donating groups─especially at the ortho position─markedly enhance bond activation via neighboring group effects. Cooperative enhancement is also demonstrated in higher-order clusters (trimers to pentamers), particularly for the stronger H-F bond, which requires greater interaction synergy to cleave. The studies on O-heterocycles highlighted the impact of electronegativity on the extent of bond activation and the requirement for additional cooperative interactions to achieve H-X bond cleavage. The ΔVn(Cl) MESP parameter shows a strong correlation with interaction energy, serving as a predictive descriptor of bond activation. These findings provide valuable insights into the remarkable ability of weak noncovalent interactions to facilitate the breaking of strong bonds, offering insights with broad implications for catalysis, molecular design, and noncovalent bond activation strategies.

PyPE_RESP: A Tool to Facilitate and Standardize Derivation of RESP Charges

We introduce PyPE_RESP, a tool to facilitate and standardize partial atomic charge derivation using the Restrained Electrostatic Potential (RESP) approach. PyPE_RESP builds upon the open-source Python package RDKit for chemoinformatics and the AMBER suite for molecular simulations. PyPE_RESP provides an easy setup of multiconformer and multimolecule RESP fitting while allowing a comprehensive definition of charge constraint groups through multiple methods. As a command line tool, PyPE_RESP can be integrated into batch processes. The software enables the derivation of partial atomic charges for additive and polarizable force fields. It outputs constraint group and nonconstraint group charges to give an immediate overview of the fit result. PyPE_RESP will be distributed with AmberTools and compatible with most computing platforms.

Exploring the molecular mechanisms of herbicide adsorption on microplastics: A quantum chemical approach

The widespread presence of microplastics in the environment has raised significant concerns, particularly regarding their potential interactions with herbicides and the combined pollution effects on ecosystems. In this study, quantum chemical calculations were employed to investigate the interaction mechanisms between polyethylene (PE) and polyvinyl chloride (PVC) microplastics and phenoxyacetic herbicides. The results revealed that PVC exhibits a stronger adsorption capacity compared to PE, and that low ionic strength conditions weaken the interactions between microplastics and herbicides. The energy decomposition analysis indicates that dispersion and electrostatic interactions are the predominant components contributing to the interaction energy, thus positioning the herbicide adsorption sites on microplastics near the minima of van der Waals and electrostatic potentials. The presence of hydrogen bond acceptors in microplastics influences the formation of intramolecular or intermolecular hydrogen bonds with the carboxylic groups of herbicides, resulting in significant changes in vibrational modes and infrared spectral absorption peaks, which offers a potential method for in situ monitoring of herbicide adsorption on microplastics. Additionally, different charge transfer phenomena are observed during the adsorption process, with PVC tending to lose electrons and PE to gain electrons. These insights provide a theoretical foundation for a deeper understanding of the adsorption behavior of phenoxyacetic herbicides on microplastics and hold significant implications for the optimization of environmental remediation strategies.

Theoretical study of the nature of σ-hole regium bond between CuX/AgX/AuX and pyridine

CONTEXT

The σ-hole regium bond complexes between coinage metal monohalide molecule CuX/AgX/AuX (X = F, Cl, and Br) and pyridine (C5H5N), which have linear orientation and perpendicular orientation, have been systematically probed at the MP2/aug-cc-pVTZ level. By comparing the calculated interaction energy, we can see that the linear orientation interactions are a little stronger than the corresponding perpendicular orientation interactions in C5H5N-CuX/AgX/AuX complexes. The binding energies for linear orientation regium bond complexes range from - 34 to - 60 kcal/mol, while those perpendicular orientation regium bond complexes are from - 24 to - 50 kcal/mol. Both types of interactions energies all tend to follow the Au > Cu > Ag order and reduced with the decrease in electronegativity F > Cl > Br in C5H5N-CuX/AgX/AuX complexes. The electrostatic energy is the major source of the attraction for the linear orientation regium bond interactions, while for the perpendicular orientation regium bond interactions are mainly due to electrostatic and induction energy.

METHODS

All the complexes and respective monomers were optimized at the MP2/aug-cc-pVTZ level. Relativistic effects were considered for Cu, Ag, Au, and Br by using the aug-cc-pVTZ-PP basis set. The NBO population analysis and AIM and IRI analysis were carried out. The interaction energies of the σ-hole regium bonds complexes were decomposed by using the symmetric adaptive perturbation theory (SAPT).

How many distinct and reliable multireference diagnostics are there?

Economical multireference (MR) diagnostics are essential for high-throughput computational studies, enabling the rapid and accurate identification of molecules affected by nondynamic correlation within large molecular datasets. Although various MR diagnostics have been proposed, benchmarking studies that help identify the criteria for an effective diagnostic are still scarce. In this article, we examine a wide range of correlation measures to evaluate their potential as MR diagnostics. We identify a small set of valid size-intensive correlation measures based on maximum metrics, exhibiting similar predictive values. Among these, we highlight INDmax, which offers an easy interpretation: it captures the largest deviation of a natural orbital occupancy from the boundary values corresponding to a single-reference wave function. No energy-based correlation measure was found suitable for constructing MR diagnostics. Finally, we demonstrate how average correlation measures, although not suitable as MR diagnostics, can provide a more comprehensive view of electron correlation within the molecule.

Investigation of the Molecular Level Interaction in [CH3OH-CH2X2] Complexes (X=I, Br, and Cl) using Matrix-Isolation IR Spectroscopy

TheCH 3 OH - CH 2 X 2 ${\left[ {{\rm{CH}}_{\rm{3}} {\rm{OH}} - {\rm{CH}}_{\rm{2}} {\rm{X}}_{\rm{2}} } \right]}$ (X=Cl, Br, and I) complexes have been studied to understand the tendency towards the formation of hydrogen bonds and halogen bonds. Three different types of interactions viz., C-X· · · ${ \cdot \cdot \cdot }$ O, C-H· · · ${ \cdot \cdot \cdot }$ O, and O-H· · · ${ \cdot \cdot \cdot }$ X, are possible between theCH 3 OH ${{\rm{CH}}_{\rm{3}} {\rm{OH}}}$ andCH 2 X 2 ${{\rm{CH}}_{\rm{2}} {\rm{X}}_{\rm{2}} }$ . Experiments have been carried out in low temperatureN 2 ${{\rm{N}}_{\rm{2}} }$ matrix using Fourier Transform Infrared spectroscopy. Electronic structure calculations have been performed to identify the possible binding motifs betweenCH 2 X 2 ${{\rm{CH}}_{\rm{2}} {\rm{X}}_{\rm{2}} }$ andCH 3 OH ${{\rm{CH}}_{\rm{3}} {\rm{OH}}}$ . Formation of more than one complex has been confirmed inCH 3 OH - CH 2 X 2 ${\left[ {{\rm{CH}}_{\rm{3}} {\rm{OH}} - {\rm{CH}}_{\rm{2}} {\rm{X}}_{\rm{2}} } \right]}$ (X=Br and I) mixture, using the experimental and simulated IR spectra, whereas only one type of complex is found inCH 3 OH - CH 2 Cl 2 ${\left[ {{\rm{CH}}_{\rm{3}} {\rm{OH}} - {\rm{CH}}_{\rm{2}} {\rm{Cl}}_{\rm{2}} } \right]}$ mixture. Energy decomposition analysis, quantum theory of atoms in molecules, and non-covalent interaction analysis have been performed to understand the nature of interaction and the driving force for complexation under experimental conditions.

Methyl formate synthesis via S N Acyl esterification on interstellar ice mantles

CONTEXT

Methyl formate (MF) has been detected in several interstellar environments, but whether or not the formation of this molecule takes place in the gas phase or on the ices of interstellar grains is still unclear. In this study, we explore the synthesis of methyl formate through the nucleophilic acyl substitution (SN Acyl) reaction between methanol (CH3 OH) and formic acid (HCOOH) on amorphous solid water, which is the main component of interstellar ice mantles.

METHODS

Using density functional theory (DFT), we model MF formation by sampling HCOOH in different catalytic sites on the water clusters with CH3 OH, and vice versa, for initial reactant configurations. We select the initial binding modes from the binding energy distributions of both reactant species. We assess the energy and synchronicity of the reaction by analyzing the reaction mechanisms through intrinsic reaction coordinate (IRC) energy, reaction force, and reaction electronic flux profiles. Using Wiberg bond order derivatives, we identify reaction events linked to hidden transition states that are encountered along the reaction coordinate.

In Silico Screening of CO2-Dipeptide Interactions for Bioinspired Carbon Capture

Carbon capture, sequestration and utilization offers a viable solution for reducing the total amount of atmospheric CO2 concentrations. On an industrial scale, amine-based solvents are extensively employed for CO2 capture through chemisorption. Nevertheless, this method is marked by the high cost associated with solvent regeneration, high vapor pressure, and the corrosive and toxic attributes of by-products, such as nitrosamines. An alternative approach is the biomimicry of sustainable materials that have strong affinity and selectivity for CO2. Bioinspired approaches, such as those based on naturally occurring amino acids, have been proposed for direct air capture methodologies. In this study, we present a database consisting of 960 dipeptide molecular structures, composed of the 20 naturally occurring amino acids. Those structures were analyzed with a novel computational workflow presented in this work that considers certain interaction sites that determine CO2 affinity. Density functional theory (DFT) and symmetry-adapted perturbation theory (SAPT) computations were performed for the calculation of CO2 interaction energies, which allowed to limit our search space to 400 unique dipeptide structures. Using this computational workflow, we provide statistical insights into dipeptides and their affinity for CO2 binding, as well as design principles that can further enhance CO2 capture through cooperative binding.

Complementary Peptide Interactions Support the Ultra-Rigidity of Polymers of De Novo Designed Click-Functionalized Bundlemers

Computationally designed 29-residue peptides yield tetra-α-helical bundles with D2 symmetry. The "bundlemers" can be bifunctionally linked via thiol-maleimide cross-links at their N-termini, yielding supramolecular polymers with unusually large, micrometer-scale persistence lengths. To provide a molecularly resolved understanding of these systems, all-atom molecular modeling and simulations of linked bundlemers in explicit solvent are presented. A search over relative orientations of the bundlemers identifies a structure, wherein at the bundlemer-bundlemer interface, interior hydrophobic residues are in contact, and α-helices are aligned with a pseudocontiguous α-helix that spans the interface. Calculation of a potential of mean force confirms that the structure in which the bundlemers are in contact and colinearly aligned is a stable minimum. Analyses of hydrogen bonds and hydrophobic complementarity highlight the complementary interactions at the interface. The molecular insight provided reveals the molecular origins of bundlemer alignment within the supramolecular polymers.

Interplay of Tetrel, Hydrogen, and Halogen Bonds in F3GeOCl and HCN Complexes: A Comprehensive Theoretical Study of Dimers, Trimers, and Tetramers

This study investigates the nature and interplay of noncovalent interactions (NCIs)─tetrel bonds (TB), hydrogen bonds (HB), and halogen bonds (XB)─in molecular assemblies formed between trifluorogermyl hypochlorite (F3GeOCl) and hydrogen cyanide (HCN). Using a combination of high-level computational methods, we explored the geometric, energetic, and electronic properties of dimers, trimers, and tetramers formed in different molar ratios of interacting reagents. Various analyses reveal a significant cooperativity between TB and HB, which mutually reinforce each other, while XB interactions are diminished in the presence of TB and HB. Energy decomposition analysis (EDA) through SAPT and sobEDAw methods identified electrostatic and orbital interactions as key contributors to the stabilization of TB and HB, while dispersion plays a prominent role in XB. A perfect linear correlation was found between interaction energy and charge density at bond critical points (BCPs), underscoring the predictive value of these metrics. These findings shed light on the cooperative nature of NCIs and provide a framework for designing molecular systems in supramolecular chemistry and crystal engineering.

Modelling Lithium-Ion Transport Properties in Sulfoxides and Sulfones with Polarizable Molecular Dynamics and NMR Spectroscopy

We present a computational study of the structure and of the transport properties of electrolytes based on Li[(CF₃SO₂)₂N] solutions in mixtures of sulfoxides and sulfones solvents. The simulations of the liquid phases have been carried out using molecular dynamics with a suitably parametrized model of the intermolecular potential based on a polarizable expression of the electrostatic interactions. Pulse field gradient NMR measurements have been used to validate and support the computational findings. Our study show that the electrolytes are characterized by extensive aggregation phenomena of the support salt that, in turn, determine their performance as conductive mediums.

Evidence of strong O-H⋯C interactions involving apical pyramidane carbon atoms as hydrogen atom acceptors

Using high-level quantum chemical calculations, we predicted a strong O-H⋯C interaction between the apical carbon atoms of pyramidane and its derivatives and water molecules. Analysis of calculated electrostatic potential maps showed that there are areas of strong negative potential above apical carbon atoms in all studied structures. The results of quantum chemical calculations showed that the O-H⋯C interaction between the hydrogen atom of water and the apical carbon atom of pyramidane derivatives with four -CH3 substituents is unexpectedly strong, ΔECCSD(T)/CBS = -7.43 kcal mol-1. The strong hydrogen bonds were also predicted in the case of unsubstituted pyramidane (ΔECCSD(T)/CBS = -6.41 kcal mol-1) and pyramidane with four -OH substituents (ΔECCSD(T)/CBS = -5.87 kcal mol-1). Although there are not many crystal structures of pyramidane-like molecules, we extracted examples of pyramidal-shaped molecules with apical carbon atoms from the Cambridge Structural Database and analyzed their hydrogen-bonding patterns. Analysis of crystal structures confirmed the existence of short non-covalent contacts between apical carbon atoms and neighboring hydrogen atoms.

Accurate Enthalpies of Formation for Bioactive Compounds from High-Level Ab Initio Calculations with Detailed Conformational Treatment: A Case of Cannabinoids

Our recently developed approach based on the local coupled-cluster with single, double, and perturbative triple excitation [LCCSD(T)] model gives very efficient means to compute the ideal-gas enthalpies of formation. The expanded uncertainty (95% confidence) of the method is about 3 kJ·mol-1 for medium-sized compounds, comparable to typical experimental measurements. Larger compounds of interest often exhibit many conformations that can significantly differ in intramolecular interactions. Although the present capabilities allow processing even a few hundred distinct conformer structures for a given compound, many systems of interest exhibit numbers well in excess of 1000. In this study, we investigate how to reduce the number of expensive LCCSD(T) calculations for large conformer ensembles while controlling the error of the approximation. The best strategy found was to correct the results of the lower-level, surrogate model (density functional theory, DFT) in a systematic manner. It was also found that the error in the conformational contribution introduced by a surrogate model is mainly driven by a systematic (bias) rather than a random component of the DFT energy deviation from the LCCSD(T) target. This distinction is usually overlooked in DFT benchmarking studies. As a result of this work, the enthalpies of formation for 20 cannabinoid and cannabinoid-related compounds were obtained. Comprehensive uncertainty analysis suggests that the expanded uncertainties of the obtained values are below 4 kJ·mol-1.

Functionalization of zeolite-encapsulated Cu5 clusters as visible-light photoactive sub-nanomaterials

The unique structural properties of zeolites make them ideal environments for encapsulating subnanometric metal clusters on their microporous channels and cavities, showing an enhanced catalytic performance. As a first step towards the functionalization of these clusters as photocatalysts as well, this work addresses the optical properties of zeolite-encapsulated Cu5-TiO2 nanoparticles as well as their application in the photo-induced activation of CO2 by sunlight. Model density functional theory (DFT) calculations indicate the stability of the Cu5 cluster adsorbed on the TiO2 nanoparticles filling the pores of a model zeolite structure. Second, it is shown that while TiO2 nanoparticles absorb in the UV, the photo-absorption spectrum of the Cu5-TiO2 nanoparticle composite is peaked at the visible region, where the sun has its maximum energy input, also allowing for the photo-induced activation of CO2 adsorbed onto the Cu5 cluster.

Dithienoarsinines: stable and planar π-extended arsabenzenes

Stable planar dithienoarsinines were synthesized and structurally characterized. These compounds exhibit monomeric structures in the solution and solid states, avoiding dimerization, even in the absence of steric protection. They exhibited high global aromaticity with 14 or 22π-electron systems. In the solid state, intermolecular interactions through arsenic atoms were observed, and As⋯As interactions resulted in aggregation-induced emission enhancement properties with a significant bathochromic shift. The W(CO)5 complex displayed a significantly distorted coordination geometry owing to arsenic cooperative stacking and hydrogen interactions, resulting in a 1D alignment of the complex. Additionally, despite their aromatic nature, dithienoarsinines undergo reactions with alkynes or benzynes to form the corresponding [4 + 2] cycloadducts. Oxygen molecules oxidize the p-position of arsinine, leading to the formation of σ-dimerized compounds while retaining the aromaticity of the arsinine ring. In contrast, oxygen attacks the phosphorus atom in phosphinine, resulting in the formation of phosphinic acid with a loss of aromaticity.

The carbonyl-sulfur chalcogen bonding interaction: Rotational spectroscopic study of the 2,2,4,4-tetrafluoro-1,3-dithietane···formaldehyde complex

The rotational spectrum of a binary molecular cluster consisting of 2,2,4,4-tetrafluoro-1,3-dithietane (C2S2F4) and formaldehyde (H2CO) was studied by means of high-resolution Fourier transform microwave spectroscopy in conjunction with quantum chemical calculations. One of the three isomers predicted at the B3LYP-D3(BJ)/def2-TZVP level of theory was successfully detected in the supersonic expansion. Theoretical analyses using the non-covalent interactions and natural bond orbital methods reveal that the observed isomer is primarily stabilized by one C=O⋯S chalcogen bond and two C-H⋯F hydrogen bonds. The distance between the oxygen atom of H2CO and the nearest sulfur atom of C2S2F4 within the observed isomer is 2.9260(1) Å and the angle ∠O⋯S-C is 161.83(1)°. The analysis utilizing the symmetry-adapted perturbation theory approach demonstrates that electrostatic interactions play a significant role in stabilizing the studied complex, with the contribution of dispersion interactions being comparable to that of electrostatic ones.

Unraveling C-Selective Ring-Opening of Phosphiranes with Carboxylic Acids and Other Nucleophiles: A Mechanistically-Driven Approach

Phosphiranes are weak Lewis bases reacting with only a limited number of electrophiles to produce the corresponding phosphiranium ions. These salts are recognized for their propensity to undergo reactions with oxygen pronucleophiles at the phosphorus site, leading to the formation of phosphine oxide adducts. Building on a thorough mechanistic understanding, we have developed an unprecedented approach that enables the selective reaction of carboxylic acids, and other nucleophiles, at the carbon site of phosphiranes. This method involves the photochemical generation of highly reactive carbenes, which react with 1-mesitylphosphirane to yield ylides. The latter undergoes a stepwise reaction with carboxylic acids, resulting in the production of the desired phosphines. In addition to DFT calculations, we have successfully isolated and fully characterized the key intermediates involved in the reaction.

End Group Effects on Anion Binding in Tetraglycine Peptide: A Computational Study

The importance of anions in various processes has led to a search for molecules that can effectively recognize and interact with these anions. This study explores how the tetraglycine [(Gly)4] peptide in its zwitterionic, neutral, and terminally capped forms acts as a receptor for H2PO4 - and HSO4 - anions within the framework of supramolecular host-guest chemistry. Using molecular dynamics (MD) simulations, we obtained the conformations of the receptor-anion complexes. Density functional theory (DFT), quantifies the complexes' interaction energies in both gas and solvent phases. Proton transfer within the zwitterionic complex with H2PO4 - anion alters peptide charge distribution, affecting its conformation and binding site arrangement, as analysed by quantum mechanics/molecular mechanics (QM/MM) methods. Symmetry-adapted perturbation theory (SAPT) and noncovalent interactions analysis highlight the role of electrostatic interactions in these receptor-anion complexes. It emphasizes the key interactions such as N-H⋅⋅⋅⋅O and O-H⋅⋅⋅O=C between the peptide backbone and anions and elucidates the molecular recognition mechanism driven by crucial noncovalent interactions. The termination of the peptide's end groups modulates anion binding sites from the backbone to the charged N-terminal, resulting in distinct binding sites. Our findings provide insights for designing peptides tailored to function as anion receptors in diverse supramolecular chemistry applications.

Acceleration without Disruption: DFT Software as a Service

Density functional theory (DFT) has been a cornerstone in computational chemistry, physics, and materials science for decades, benefiting from advancements in computational power and theoretical methods. This paper introduces a novel, cloud-native application, Accelerated DFT, which offers an order of magnitude acceleration in DFT simulations. By integrating state-of-the-art cloud infrastructure and redesigning algorithms for graphic processing units (GPUs), Accelerated DFT achieves high-speed calculations without sacrificing accuracy. It provides a user-friendly and scalable solution for the increasing demands of DFT calculations in scientific communities. The implementation details, examples, and benchmark results illustrate how Accelerated DFT can significantly expedite scientific discovery across various domains.

DensToolKit2: A comprehensive open-source package for analyzing the electron density and its derivative scalar and vector fields

In this article, we provide details of the suite DensToolKit-v2, which consists of a set of cross-platform, optionally parallelized programs for analyzing the molecular electron density (ρ), as well as different fields and chemical indices derived from it. Notably, with this version, the user can compute the Non-Covalent Interaction index, the Density Overlap Regions Index, and fields related to single-spin-type molecular orbitals, such as the spin density. In addition, DensToolKit-v2 includes several programs for analyzing other less-known fields, such as the Density Matrix of order 1, the two-electron pair density function, and the Fourier transforms of these fields, that is, functionals in momentum space. A new sub-program to compute integrated properties of each of the fields released in the suite is included. A simple graphical user interface is released, which eases the visualization of ρ critical points topology. Most interestingly, this version includes a program that renders estimations of pKa's of carboxylic acids and pKb's of amines (primary, secondary, and tertiary) through refined relations between experimental data and the molecular electrostatic potential computed at isosurfaces of ρ. Details related to the speed of the programs and a few examples of how to use the program in workflows are discussed, and the source code is released through a git repository under the GPLv3 terms.

The C-H···S-S hydrogen bonding in diethyl disulfide⋯difluoromethane: a combined microwave spectroscopic and computational study

The C-H⋯S weak interaction is crucial for comprehending the stability in biological macromolecules and their interactions with smaller molecules. Despite its prevalence, an in-depth understanding and recognition of such interaction remain elusive. Herein, the rotational spectra of a binary complex formed by diethyl disulfide and difluoromethane were investigated using Fourier transform microwave spectroscopy combined with theoretical calculations to examine the C-H⋯S-S interaction. The most stable conformation observed experimentally is stabilized by one C-H⋯S-S hydrogen bond and two weaker C-H⋯F hydrogen bonds. Non-covalent interaction, natural bond orbital, and symmetry-adapted perturbation theory methods were employed to describe the intermolecular interactions within the adduct. Experiments indicated H⋯F and H⋯S distances of 2.68(7) Å and 2.64(1) Å, respectively, with bonding angles of 121.0(4)° for C-H⋯F and 135.3(6)° for C-H⋯S hydrogen bonds. The geometric characteristics and theoretical analyses suggest that the C-H⋯S-S hydrogen bond is the predominant interaction, contributing an energy of 7.6 kJ mol-1. Additionally, the C-H⋯F hydrogen bond also contributes to the stability of the complex, contributing approximately 2.6 kJ mol-1. London dispersion is a primary factor in the stability of complexes, contributing 53% to the total attractive interaction. The results indicate that non-traditional hydrogen bond participants, such as C-H groups and S-S linkages, can form hydrogen bonds and fluorination enhances the interactions.

Computational Library Enables Pattern Recognition of Noncovalent Interactions and Application as a Modern Linear Free Energy Relationship

A quantitative and predictive understanding of how attractive noncovalent interactions (NCIs) influence functional outcomes is a long-standing goal in mechanistic chemistry. In that context, better comprehension of how substituent effects influence NCI strengths, and the origin of those effects, is still needed. We sought to build a resource capable of elucidating fundamental origins of substituent effects in NCIs and diagnosing NCIs in chemical systems. To accomplish this, a library of 893 NCI energies was calculated encompassing cation-π, anion-π, CH-π, and π-π interactions across 60 different arenes and heteroarenes. The interaction energies (IEs) were calculated using symmetry-adapted perturbation theory (SAPT), which identifies electrostatic, inductive, exchange-repulsive, and dispersive contributions to total IE. This descriptor library provides a comprehensive platform for evaluating substituent effect trends beyond traditional molecular descriptors such as Hammett values, frontier molecular orbital energies, and electrostatic potential, thereby expanding the tools available to analyze modern chemical processes that involve NCIs. To demonstrate the application of this library, three case studies in asymmetric catalysis and supramolecular chemistry are presented. These case studies informed the development of an automated NCI analysis tool, which employs statistical analyses to diagnose a particular NCI in a chemical system of interest.

Unraveling the Strength and Nature of Se∙∙∙O Chalcogen Bonds: A Comparative Study of SeF2 and SeF4 Interactions with Oxygen-Bearing Lewis Bases

Chalcogen bonds (ChBs) involving selenium have attracted substantial scholarly interest in past years owing to their fundamental roles in various chemical and biological fields. However, the effect of the valency state of the electron-deficient selenium atom on the characteristics of such ChBs remains unexplored. Herein, we comparatively studied the σ-hole-type Se∙∙∙O ChBs between SeF2/SeF4 and a series of oxygen-bearing Lewis bases, including water, methanol, dimethyl ether, ethylene oxide, formaldehyde, acetaldehyde, acetone, and formic acid, using ab initio computations. The interaction energies of these chalcogen-bonded heterodimers vary from -5.25 to -11.16 kcal/mol. SeF2 participates in a shorter and stronger ChB than SeF4 for all the examined heterodimers. Such Se∙∙∙O ChBs are closed-shell interactions, exhibiting some covalent character for all the examined heterodimers, except for SeF4∙∙∙water. Most of these chalcogen-bonded heterodimers are predominantly stabilized through orbital interactions between the lone pair of the O atom in Lewis bases and the σ*(Se-F) antibonding orbitals of Lewis acids. The back-transfer of charge from the lone pair of selenium into the σ* or π* antibonding orbitals of Lewis bases is also observed for all systems. Energy decomposition analysis reveals that the electrostatic component significantly stabilizes the targeted heterodimers, while the induction and dispersion contributions cannot be ignored.

A DFT investigation on the potential of beryllium oxide (Be12O12) as a nanocarrier for nucleobases

The study of the interactions between biomolecules and nanostructures is quite fascinating. Herein, the adsorption propensity of beryllium oxide (Be12O12) nanocarrier toward nucleobases (NBs) was investigated. In terms of DFT calculations, the adsorption tendency of Be12O12 toward NBs, including cytosine (NB-C), guanine (NB-G), adenine (NB-A), thymine (NB-T), and uracil (NB-U), was unveiled through various configurations. Geometrical, electronic, and energetic features for Be12O12, NBs, and their associated complexes were thoroughly evaluated at M06-2X/6-311+G** level of theory. The potent adsorption process within NBs∙∙∙Be12O12 complexes was noticed through favorable interaction (Eint) and adsorption (Eads) energies with values up to -53.04 and -38.30 kcal/mol, respectively. Generally, a significant adsorption process was observed for all studied complexes, and the favorability followed the order: NB-C∙∙∙ > NB-G∙∙∙ > NB-A∙∙∙ > NB-T∙∙∙ > NB-U∙∙∙Be12O12 complexes. Out of all studied complexes, the most potent adsorption was found for NB-C∙∙∙Be12O12 complex within configuration A (Eint = -53.04 kcal/mol). In terms of energy decomposition, SAPT analysis revealed electrostatic (Eelst) forces to be dominant within the studied adsorption process with values up to -99.88 kcal/mol. Analyzing QTAIM and NCI, attractive intermolecular interactions within the studied complexes were affirmed. From negative values of thermodynamic parameters, the nature of the considered adsorption process was revealed to be spontaneous and exothermic. Regarding density of state, IR, and Raman analyses, the occurrence of the adsorption process within NBs∙∙∙Be12O12 complexes was confirmed. Noticeable short recovery time values were observed for all studied complexes, confirming the occurrence of the desorption process. The findings provided fundamental insights into the potential application of Be12O12 nanocarrier in drug and gene delivery processes.

Support effects on conical intersections of Jahn-Teller fluxional metal clusters on the sub-nanoscale

The concept of fluxionality has been invoked to explain the enhanced catalytic properties of atomically precise metal clusters of subnanometer size. Cu3 isolated in the gas phase is a classical case of a fluxional metal cluster where a conical intersection leads to a Jahn-Teller (JT) distortion resulting in a potential energy landscape with close-lying multiminima and, ultimately, fluxional behavior. In spite of the role of conical intersections in the (photo)stability and (photo)catalytic properties of surface-supported atomic metal clusters, they have been largely unexplored. In this work, by applying a high-level multi-reference ab initio method aided with dispersion corrections, we analyze support effects on the conical intersection of Cu3 considering benzene as a model support molecule of carbon-based surfaces. We verify that the region around the conical intersection and the associated Jahn-Teller (JT) distortion is very slightly perturbed by the support when the Cu3 cluster approaches it in a parallel orientation: Two electronic states remain degenerate for a structure with C3 symmetry consistent with the D3h symmetry of unsupported Cu3 at the conical intersection. It extends over a one-dimensional seam that characterizes a physisorption minimum of the Cu3-benzene complex. The fluxionality of the Cu3 cluster, reflected in large fluctuations of relaxed Cu-Cu distances as a function of the active JT mode, is kept unperturbed upon complexation with benzene as well. In stark contrast, for the energetically favored perpendicular orientation of the Cu3 plane to the benzene ring plane, the conical intersection (CI) is located 12 100 cm-1 (∼1.5 eV) above the chemisorption minimum, with the fluxionality being kept at the CI's nearby and lost at the chemisorption well. The first excited state at the perpendicular orientation has a deep well (>4000 cm-1), being energetically closer to the CI. The transition dipole moment between ground and excited states has a significant magnitude, suggesting that the excited state can be observed through direct photo-excitation from the ground state. Besides demonstrating that the identity of an isolated Jahn-Teller metal cluster can be preserved against support effects at a physisorption state and lifted out at a chemisorption state, our results indicate that a correlation exists between conical intersection topography and fluxionality in the metal cluster's Cu-Cu motifs.

Adsorption and desorption of parachlormetaxylenol by aged microplastics and molecular mechanism

The addition of active ingredients such as antibacterial agent and non-active ingredients such as plastic microspheres (MPs) in personal care products (PCPs) are the common pollutants in the aquatic environment, and their coexistence poses potential threat to the aquatic ecosystem. As a substitute for the traditional antibacterial ingredients triclosan and triclocarban, the usage of parachlormetaxylenol (PCMX) is on the rise and is widely used in PCPs. In this study, the adsorption and desorption behaviors of PCMX were investigated with two typical MPs, polyvinyl chloride (PVC) and polyethylene (PE), and the effects of different aging modes and molecular mechanisms were explored through batch experiments and density functional theory calculation. Both laboratory aging and field aging resulted in surface wrinkles of MPs, along with an increased proportion of oxygen-containing functional groups (CO, -OH). At the same aging time, the degree of laboratory aging was stronger than that of field aging, and the aging degree of PVC was greater that of PE. The aging process enhanced the adsorption capacity of MPs for PCMX. The equilibrium adsorption capacity of PVC increased from 3.713 mg/g (virgin) to 3.823 mg/g (field aging) and 3.969 mg/g (laboratory aging), while that of PE increased from 3.509 mg/g to 3.879 mg/g and 4.109 mg/g, respectively. Meanwhile, aging also resulted in an increase in the desorption capacity of PCMX from PVC and PE. Oxygen-containing functional groups in aged MPs could serve as adsorption sites for PCMX and improved the electrostatic adsorption capacity. Oxygen-containing groups generated on the surface of aged MPs formed hydrogen bonding with the phenolic hydroxyl groups of PCMX, which became the main driving force for adsorption. Our results reveal the potential impact and mechanism of aging on the adsorption of PCMX by MPs, which provides new insights for the interaction mechanism between environmental MPs and associated contaminants.

Intermolecular interaction energies with AROFRAG-A systematic approach for fragmentation of aromatic molecules

Intermolecular interactions with polycyclic aromatic hydrocarbons (PAHs) represent an important area of physisorption studies. These investigations are often hampered by a size of interacting PAHs, which makes the calculation prohibitively expensive. Therefore, methods designed to deal with large molecules could be helpful to reduce the computational costs of such studies. Recently we have introduced a new systematic approach for the molecular fragmentation of PAHs, denoted as AROFRAG, which decomposes a large PAH molecule into a set of predefined small PAHs with a benzene ring being the smallest unbreakable unit, and which in conjunction with the Molecules-in-Molecules (MIM) approach provides an accurate description of total molecular energies. In this contribution we propose an extension of the AROFRAG, which provides a description of intermolecular interactions for complexes composed of PAH molecules. The examination of interaction energy partitioning for various test cases shows that the AROFRAG3 model connected with the MIM approach accurately reproduces all important components of the interaction energy. An additional important finding in our study is that the computationally expensive long-range electron-correlation part of the interaction energy, that is, the dispersion component, is well described at lower AROFRAG levels even without MIM, which makes the latter models interesting alternatives to existing methods for an accurate description of the electron-correlated part of the interaction energy.

Bridging the Gap in the Structure-Function Paradigm of Enzymatic PET Degradation-Aromatic Residue Driven Balanced Interactions with Catalytic and Anchoring Subsite

Understanding all parameters contributing to enzyme activity is crucial in enzyme catalysis. For enzymatic PET degradation, this involves examining the formation of the enzyme-PET complex. In IsPETase (WT), a PET-degrading enzyme from Ideonella sakaiensis, mutating two non-catalytic residues (DM) significantly enhances activity. Such mutations, depending on their position in the tertiary structure, fine-tune enzyme function. However, detailed molecular insights into these mutations' structure-function relationship for PET degradation are lacking. This study characterizes IsPETase's catalytic ability compared to WT TfCut2 using molecular dynamics simulations and quantum mechanical methods. We explore the conformational landscape of the enzyme-PET complex and quantify residue-wise interaction energy. Notably, aromatic and hydrophobic residues Tyr, Trp, and Ile in the catalytic subsite S1, and aromatic Phe and polar Asn in the anchoring subsite S3, crucially optimize PET binding. These residues enhance PET specificity over non-aromatic plastics. Our findings suggest that the balance between binding at subsite S1 and subsite S3, which is influenced by cooperative mutations, underlies catalytic activity. This balance shows a positive correlation with experimentally obtained kcat/Km values: WT TfCut2 Collapse

Key Words

• Cooperative effect
• Enzyme catalysis
• IsPETase
• Molecular dynamics
• Mutation

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MESH Headings

• Molecular Dynamics Simulation
• Polyethylene Terephthalates/chemistry
• Polyethylene Terephthalates/metabolism
• Catalytic Domain
• Structure-Activity Relationship
• Burkholderiales/enzymology
• Biocatalysis
• Mutation
• Bacterial Proteins/chemistry
• Bacterial Proteins/metabolism
• Bacterial Proteins/genetics

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Grants

• CRG/2019/002891 DST
• SPG/2022/001350 DST
• SIR/2022/000924 DST
• University of Calicut

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Affiliation(s)

Anjima James Department of Applied Chemistry, Cochin University of Science and Technology, Thrikakkara, Kochi, Kerala, 682 022, India
Anjitha Bhasi Department of Applied Chemistry, Cochin University of Science and Technology, Thrikakkara, Kochi, Kerala, 682 022, India
Susmita De Department of Chemistry, University of Calicut, Calicut University P.O., Malappuram, Kerala, 673 635, India

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Collaborators Collapse

Synergistic Intramolecular Non-Covalent Interactions Enable Robust Pure-Blue TADF Emitters

Stability-issues of organic light-emitting diodes (OLEDs) employing thermally activated delayed fluorescence (TADF) require further advancements, especially in pure-blue range of CIEy < 0.20, existing a dilemma between color purity and device lifetime. Though improving bond-dissociation-energy (BDE) can effectively improve material intrinsic stability, strategies to simultaneously improve BDE and photophysical performances are still lacking. Herein, it is disclosed that synergistic intramolecular non-covalent interactions (Intra-NI) can achieve not only the highest C─N BDE among blue TADF materials, but enhanced molecular-rigidity, near-unity photoluminescent quantum yields and short delayed lifetime. Pure-blue TADF-OLEDs based on proof-of-concept TADF material realize high external-quantum-efficiency and record-high LT80@500 cd m-2 of 109 h with CIEy = 0.16. Furthermore, deep-blue TADF-sensitized devices exhibit high LT80@500 cd m-2 of 81 h with CIEy = 0.10. The findings provide new insight into the critical role of Intra-NI in OLED materials and open the way to tackling vexing stability issues for developing robust pure-blue organic emitters and other functional materials.

Describing the Disulfide Bond: From the Density Functional Theory and Back through the "Lego Brick" Approach

Selected molecular species containing the disulfide bond, RSSR, have been considered, these ranging from hydrogen disulfide, H2S2 (R = H), to diphenyl disulfide with R = C6H5. The aim of this work is two-fold: (i) to investigate different computational approaches in order to derive accurate equilibrium structures at an affordable cost, (ii) to employ the results from the first goal in order to benchmark cheaper methodologies rooted in the density functional theory. Among the strategies used for the accurate geometrical determinations, the semiexperimental approach has been exploited in combination with a reduced-dimensionality VPT2 model, without however obtaining satisfactory results. Instead, the so-called "Lego brick" approach turned out to be very effective despite the flexibility of the systems investigated. Concerning the second target of this work, the focus was mainly on the S-S bond and the structural parameters related to it. Among those tested, PBE0(-D3BJ), M06-2X(-D3) and DSD-PBEP86-D3BJ have been found to be the best-performing functionals.

Solvent Effect on Cation&otimes;3π Interactions: A First-Principles Study

Cation⊗3π interactions play a special role in the behaviors of biological molecules and carbon-based materials in aqueous solutions, yet the effects of solvation on these interactions remain poorly understood. This study examines the sequential attachment of water molecules to cation⊗3π systems (cation = Li⁺, Na⁺, K⁺), revealing that solvation influences interaction strengths in opposing ways: solvation of the metal cation decreases the strengths of cation⊗3π interactions, while the solvation of the benzene molecule increases the strengths of cation⊗3π interactions, compared with the strengths of cation⊗3π interactions in the gas phase. The mechanism analyses revealed that in the presence of surrounding water molecules, the stability of cation⊗3π systems is generally enhanced by cation-π, π-π, water-π, and water-ion interactions, while water-water interactions typically have a destabilizing effect. In addition, the primary effect of water molecules at different adsorption sites is to modulate the Coulombic multipole-multipole interactions and the overlap between monomeric charge distributions, thereby influencing the changes in strengths of cation⊗3π interactions. Moreover, AIMD simulations further underscore the practical significance of cation⊗3π interactions. These findings provide valuable insights into the structures and the strengths of cation⊗3π interactions with the effect of solvation.

Refinement of the Drude Polarizable Force Field for Hexose Monosaccharides: Capturing Ring Conformational Dynamics with Enhanced Accuracy

We present a revised version of the Drude polarizable carbohydrate force field (FF), focusing on refining the ring and exocyclic torsional parameters for hexopyranose monosaccharides. This refinement addresses the previously observed discrepancies between calculated and experimental NMR 3J coupling values, particularly in describing ring dynamics and exocyclic rotamer populations within major hexose monosaccharides and their anomers. Specifically, α-MAN, β-MAN, α-GLC, β-GLC, α-GAL, β-GAL, α-ALT, β-ALT, α-IDO, and β-IDO were targeted for optimization. The optimization process involved potential energy scans (PES) of the ring and exocyclic dihedral angles computed using quantum mechanical (QM) methods. The target data for the reoptimization included PES of the inner ring dihedrals (C1-C2-C3-C4, C2-C3-C4-C5, C5-O5-C1-C2, C4-C5-O5-C1, O5-C1-C2-C3, C3-C4-C5-O5) and the exocyclic torsions, other than the pseudo ring dihedrals (O1-C1-O5-C5, O2-C2-C1-O5, and O4-C4-C5-O5) and hydroxyl torsions used in the previous parametrization efforts. These parameters, in conjunction with previously developed Drude parameters for hexopyranose monosaccharides, were validated against experimental observations, including NMR data and conformational energetics, in aqueous environments. The resulting polarizable model is shown to be in good agreement with a range of QM data, experimental NMR data, and conformational energetics of monosaccharides in aqueous solutions. This offers a significant improvement of the Drude carbohydrate force field, wherein the refinement enhances the accuracy of accessing the conformational dynamics of carbohydrates in biomolecular simulations.

Impact of Protonation Sites on Collision-Induced Dissociation-MS/MS Using CIDMD Quantum Chemistry Modeling

Protonation is the most frequent adduct found in positive electrospray ionization collision-induced mass spectra (CID-MS/MS). In a parallel report Lee, J. J. Chem. Inf. Model. 2024, 10.1021/acs.jcim.4c00760, we developed a quantum chemistry framework to predict mass spectra by collision-induced dissociation molecular dynamics (CIDMD). As different protonation sites affect fragmentation pathways of a given molecule, the accuracy of predicting tandem mass spectra by CIDMD ultimately depends on the choice of its protomers. To investigate the impact of molecular protonation sites on MS/MS spectra, we compared CIDMD-predicted spectra to all available experimental MS/MS spectra by similarity matching. We probed 10 molecules with a total of 43 protomers, the largest study to date, including organic acids (sorbic acid, citramalic acid, itaconic acid, mesaconic acid, citraconic acid, and taurine) as well as aromatic amines including uracil, aniline, bufotenine, and psilocin. We demonstrated how different protomers can converge different fragmentation pathways to the same fragment ions but also may explain the presence of different fragment ions in experimental MS/MS spectra. For the first time, we used in silico MS/MS predictions to test the impact of solvents on proton affinities, comparing the gas phase and a mixture of acetonitrile/water (1:1). We also extended applications of in silico MS/MS predictions to investigate the impact of protonation sites on the energy barriers of isomerization between protomers via proton transfer. Despite our initial hypothesis that the thermodynamically most stable protomer should give the best match to the experiment, we found only weak inverse relationships between the calculated proton affinities and corresponding entropy similarities of experimental and CIDMD-predicted MS/MS spectra. CIDMD-predicted mechanistic details of fragmentation reaction pathways revealed a clear preference for specific protomer forms for several molecules. Overall, however, proton affinity was not a good predictor corresponding to the predicted CIDMD spectra. For example, for uracil, only one protomer predicted all experimental MS/MS fragment ions, but this protomer had neither the highest proton affinity nor the best MS/MS match score. Instead of proton affinity, the transfer of protons during the electrospray process from the initial protonation site (i.e., mobile proton model) better explains the differences between the thermodynamic rationale and experimental data. Protomers that undergo fragmentation with lower energy barriers have greater contributions to experimental MS/MS spectra than their thermodynamic Boltzmann populations would suggest. Hence, in silico predictions still need to calculate MS/MS spectra for multiple protomers, as the extent of distributions cannot be readily predicted.

Predicting Collision-Induced-Dissociation Tandem Mass Spectra (CID-MS/MS) Using Ab Initio Molecular Dynamics

Compound identification is at the center of metabolomics, usually by comparing experimental mass spectra against library spectra. However, most compounds are not commercially available to generate library spectra. Hence, for such compounds, MS/MS spectra need to be predicted. Machine learning and heuristic models have largely failed except for lipids. Here, quantum chemistry software can be used to predict mass spectra. However, quantum chemistry predictions for collision induced dissociation (CID) mass spectra in LC-MS/MS are rare. We present the CIDMD (Collision-Induced Dissociation via Molecular Dynamics) framework to model CID-based MS/MS spectra. It uses first-principles molecular dynamics (MD) to simulate the physical process of molecular collisions in CID tandem mass spectrometry. First, molecular ions are constructed at specific protonation sites. Using density functional theory, these protonated ions are targeted by argon collider gas atoms at user-specified velocities. Subsequent bond breakages are simulated over time for at least 1,000 fs. Each simulation is repeated multiple times from various collisional directions. Fragmentations are accumulated over those repeated collisions to generate CIDMD in silico mass spectra. Twelve small metabolites (<205 Da) were selected to test the accuracy of this framework in comparison to experimental MS/MS spectra. When testing different protomers, collider velocities, number of simulations, simulation time and impact factor b cutoffs, we yielded 261 predicted mass spectra. These in silico spectra resulted in entropy similarity scores of an average 624 ± 189 for all 261 spectra compared to their corresponding experimental spectra, which improved to 828 ± 77 when using optimal parameters of the most probable protomers for 12 molecules. With increasing molecular mass, higher velocities achieved better results. Similarly, different protomers showed large differences in fragmentation; hence, with increasing numbers of protomers and tautomers, the average CIDMD prediction accuracy decreased. Mechanistic details showed that specific fragment ions can be produced from different protomers via multiple fragmentation pathways. We propose that CIDMD is a suitable tool to predict mass spectra of small metabolites like produced by the gut microbiome.

A Critical Evaluation of the Hybrid KS DFT Functionals Based on the KS Exchange-Correlation Potentials

We have developed a critical methodology for the evaluation of the quality of hybrid exchange-correlation (XC) density functional approximations (DFAs) based on very fundamental quantities, i.e., Kohn-Sham (KS) XC potentials, self-consistent electron densities, first ionization potentials (IPs), and total energies. Since the XC potentials, the primary objects in the current study, are not directly accessible for the hybrids, we calculate them by inverting the KS electron densities. Utilizing this methodology, we tested 155 hybrid DFAs available in the LIBXC library using FCI and CCSD(T) methods as a reference. We have found that a group of functionals produces very decent XC potentials, mainly those with a large mixture of Hartree-Fock exchange. Moreover, the value of IP strongly depends on the XC potential quality. On the other hand, we show that the XC energy is dominated by functional-driven error, which in some cases leads to substantial errors in electronic densities. The study shows new directions for constructing more accurate XC functionals within the KS-DFT framework.

Deciphering Stereoselectivity in Hurd-Claisen Rearrangements: A Comprehensive Study of Electrostatic Interactions from Shubin's Energy Decomposition Analysis

In this study, we explore the stereoselectivity of Hurd-Claisen Rearrangements, focusing on the influence of two electron-withdrawing groups and eight diverse substituents. Utilizing the Curtin-Hammett principle, we performed energy calculations for reactions, products, and transition states using the M062X/def2TZVPP compound model. Our analysis reveals that kinetic factors predominantly dictate the reaction equilibrium. A key aspect of our research is the application of Shubin's energy decomposition analysis to optimized transition states, highlighting the significant role of electrostatic interactions in determining stereoselectivity. We further dissected each transition state into four fragments: the electron-withdrawing groups (C O 2 E t ${CO_2 Et}$ ,C N ${CN}$ ), the Hurd group ( H ${H}$ ), various substituents (C H 3 ${CH_3 }$ ,E t ${Et}$ ,S P r o p ${SProp}$ ,T B u t ${TBut}$ ,I s o B u t ${IsoBut}$ ,N H 2 P h ${NH_2 Ph}$ ,N O 2 P h ${NO_2 Ph}$ ,P h ${Ph}$ ), and the central fragment. This fragmentation approach enabled an in-depth analysis of group dipole moments, providing insights into the electrostatic forces at play. Our findings shed light on the intricate mechanisms driving stereoselectivity in Hurd-Claisen Rearrangements and enhance the understanding of molecular interactions, offering valuable implications for organic synthesis.

A practical post-Hartree-Fock approach describing open-shell metal cluster-support interactions. Application to Cu3 adsorption on benzene/coronene

Current advances in synthesizing and characterizing atomically precise monodisperse metal clusters (AMCs) at the subnanometer scale have opened up fascinating possibilities in designing new heterogeneous (photo)catalysts as well as functional interfaces between AMCs and biologically relevant molecules. Understanding the nature of AMC-support interactions at molecular-level is essential for optimizing (photo)catalysts performance and designing novel ones with improved properties. Møller-Plesset second-order perturbation theory (MP2) is one of the most cost-efficient single-reference post-Hartree-Fock wave-function-based theories that can be applied to AMC-support interactions considering adequate molecular models of the support, and thus complementing state-of-the-art dispersion-corrected density functional theory. However, the resulting AMC-support interaction is typically overestimated with the MP2 method and must be corrected. The coupled MP2 (MP2C) scheme replacing the uncoupled Hartree-Fock dispersion energy by a coupled dispersion contribution, has been proven to describe accurately van-der-Waals (vdW)-dominated interactions between closed-shell AMCs and carbon-based supports. In this work, the accuracy of a MP2C-based scheme is evaluated in modelling open-shell AMC-cluster interactions that imply charge transfer or other strong attractive energy contributions beyond vdW forces. For this purpose, we consider the interaction of Cu3 with molecular models of graphene of increasing size (benzene and coronene). In this way, it is shown that subchemical precision (within 0.1 kcal mol-1) is achieved with the modified MP2C scheme, using the explicitly correlated coupled cluster theory with single, double, and perturbative triple excitations [CCSD(T)-F12] as a benchmark method. It is also revealed that the energy difference between uncoupled and coupled dispersion terms closely follows benchmark values of the repulsive intramonomer correlation contribution. The proposed open-shell MP2C-based approach is expected to be of general applicability to open-shell atomic or molecular species interacting with coronene for regions of the potential landscape where single-reference electronic structure descriptions suffice.

Attractive acceptor-acceptor interactions in self-complementary quadruple hydrogen bonds for molecular self-assembly

Molecular self-assembly provides the means for creating large supramolecular structures, extending beyond the capability of standard chemical synthesis. To harness the power of self-assembly, it is necessary to understand its driving forces. A potent method is to exploit self-complementary hydrogen bonding, where a molecule interacts with its own copy by suitable positions of hydrogen-bond donor (D) and acceptor (A) groups. With four hydrogen bonds, there are two possible self complementary patterns: the DDAA/AADD and the DADA/ADAD motifs. Of these, the DDAA pattern is usually more stable. The traditional explanation assumes that the secondary interactions between equal groups, that is, between donors (D⋯D) or acceptors (A⋯A), are repulsive. DDAA arrays would then have two, and DADA arrays six repulsive interactions. Here, using high-end quantum chemical analysis, we show that contrary to the traditional explanation, the secondary A⋯A interactions are, in fact, attractive. We revise the model of secondary interactions accordingly.

Transition State Stabilizing Effects of Oxygen and Sulfur Chalcogen Bond Interactions

Non-covalent chalcogen bond (ChB) interactions have found utility in many fields, including catalysis, organic semiconductors, and crystal engineering. In this study, the transition stabilizing effects of ChB interactions of oxygen and sulfur were experimentally measured using a series of molecular rotors. The rotors were designed to form ChB interactions in their bond rotation transition states. This enabled the kinetic influences to be assessed by monitoring changes in the rotational barriers. Despite forming weaker ChB interactions, the smaller chalcogens were able to stabilize transition states and had measurable kinetic effects on the rotational barriers. Sulfur stabilized the bond rotation transition state by as much as -7.2 kcal/mol without electron-withdrawing groups. The key was to design a system where the sulfur σ ${\sigma }$ -hole was aligned with the lone pairs of the chalcogen bond acceptor. Oxygen rotors also could form transition state stabilizing ChB interactions but required electron-withdrawing groups. For both oxygen and sulfur ChB interactions, a strong correlation was observed between transition state stabilizing abilities and electrostatic potential (ESP) of the chalcogen, providing a useful predictive parameter for the rational design of future ChB systems.

Bis-chalcones obtained via one-pot synthesis as the anti-neurodegenerative agents and their effect on the HT-22 cell line

In the area of research on neurodegenerative diseases, the current challenge is to search for appropriate research methods that would detect these diseases at the earliest possible stage, but also new active structures that would reduce the rate of the disease progression and minimize the intensity of their symptoms experienced by the patient. The chalcones are considered in the context of candidates for new drugs dedicated to the fight against neurodegenerative diseases. The synthesis of bis-chalcone derivatives (3a-3d), as aim molecules was performed. Their structures were established by applying 1H NMR, 13C NMR, MS, FT-IR and UV-Vis spectra. All bis-chalcones were synthesized from terephthalaldehyde and appropriate aromatic ketone as substrates in the Claisen-Schmidt condensation method and evaluated in the biological tests and in silico analysis. Compounds exerted antioxidant activity using the HORAC method (3a-3d) and decreased the activities of GPx, COX-2 (3b-3d), GR (3a-3c) and CAT (3a,3b). The high anti-neurodegenerative potential of all four bis-chalcones was observed by inhibition of acetyl- (AChE) and butyrylcholinesterase (BChE) and a positive effect on the mouse hippocampal neuronal HT-22 cell line (LDH release and PGC-1α, PPARγ and GAPDH protein expression). TD-DFT method (computing a number of descriptors associated with HOMO-LUMO electron transition: electronegativity, chemical hardness and potential, first ionization potential, electron affinity) was employed to study the spectroscopic properties. This method showed that the first excited state of compounds was consistent with their maximum absorption in the computed UV-Vis spectra, which showed good agreement with the experimental spectrum using PBE1PBE functional. Using in silico approach, interactions of bis-chalcones with selected targets (aryl hydrocarbon receptor (AhR) PAS-A Domain, ligand binding domain of human PPAR-γ, soman-aged human BChE-butyrylthiocholine complex, Torpedo californica AChE:N-piperidinopropyl-galanthamine complex and the COX-2-celecoxib complex) were characterized. Results obtained in in silico models were consistent with in vitro experiments.

Kohn-Sham fragment energy decomposition analysis

We introduce the concept of Kohn-Sham fragment localized molecular orbitals (KS-FLMOs), which are Kohn-Sham molecular orbitals (MOs) localized in specific fragments constituting a generic molecular system. In detail, we minimize the local electronic energies of various fragments, while maximizing the repulsion between them, resulting in the effective localization of the MOs. We use the developed KS-FLMOs to propose a novel energy decomposition analysis, which we name Kohn-Sham fragment energy decomposition analysis, which allows for rationalizing the main non-covalent interactions occurring in interacting systems both in vacuo and in solution, providing physical insights into non-covalent interactions. The method is validated against state-of-the-art energy decomposition analysis techniques and with high-level calculations.

Unraveling the Disulfide-Carbonyl n → π* Interactions in a Gas Phase Molecular Complex and Proteins

The weak contacts between disulfide linkages and carbonyl groups are anticipated to be important in determining the structure and function of enzymes and proteins. However, the characteristics of the disulfide-carbonyl n → π* (nSS → π* C═O) interactions remain unexplored. Herein, we investigated the nSS → π* C═O interactions in the gas phase and in proteins. Rotational spectroscopic investigation of a model complex of allyl methyl disulfide with formaldehyde identified two structures, both of which are stabilized through a dominant nSS → π* C═O interaction. Surveys of the Protein Data Bank revealed the occurrence of 18 675 nSS → π* C═O interactions associated with 15 320 disulfide bonds in 7105 protein structures. Further theoretical analyses characterize the bonding nature of the nSS → π* C═O interactions. This study provides an in-depth understanding of the stabilizing effect of the nSS → π* C═O interactions in small molecular complexes and biomacromolecules.

Excited-State Dynamics in Segregated Donor-Acceptor Stacks Versus a Peri-Bisdonor-Acceptor System

The investigation of impact of through-space/through-bond electronic interaction among chromophores on photoexcited-state properties has immense potential owing to the distinct emergent photophysical pathways. Herein, the photoexcited-state dynamics of homo-sorted π-stacked aggregates of a naphthalenemonoimide and perylene-based acceptor-donor (NI-Pe) system and a fork-shaped acceptor-bisdonor (NI-Pe2) system possessing integrally stacked peri-substituted donors was examined. Femtosecond transient absorption (fsTA) spectra of NI-Pe monomer recorded in chloroform displayed spectroscopic signatures of the singlet state of Pe; 1Pe*, the charge-separated state; NI-⋅-Pe+⋅, and the triplet state of Pe; 3Pe*. The examination of ultrafast excited-state processes of NI-Pe aggregate in chloroform revealed faster charge recombination (τ C R a ${{\tau }_{CR}^{a}}$ =1.75 ns) than the corresponding monomer (τ C R m ${{\tau }_{CR}^{m}}$ =2.46 ns) which was followed by observation of a broad structureless band attributed to an excimer-like state. The fork-shaped NI-Pe2 displayed characteristic spectroscopic features of the NI radical anion (λmax~450 nm) and perylene dimer radical cation (λmax~520 nm) upon photoexcitation in non-polar toluene solvent in the nanosecond transient absorption (nsTA) spectroscopy. The investigation highlights the significance of intrinsic close-stacked arrangement of donors in ensuring a long-lived photoinduced charge-separated state (τ C R ${{\tau }_{CR}}$ =1.35 μs) in non-polar solvents via delocalization of radical cation between the donors.

Investigating the Effect of Chemical Modifications on the Ribose Sugar Conformation, Watson-Crick Base Pairing, and Intrastrand Stacking Interactions: A Theoretical Approach

Over the last few decades, chemically modified sugars have been incorporated into nucleic acid-based therapeutics to improve their pharmacological potential. Chemical modification can influence the sugar conformation, Watson-Crick hydrogen (W-C) bonding, and nucleobase stacking interactions, which play major roles in the structural integrity and dynamic properties of nucleic acid duplexes. In this study, we categorized 33 uridine (U*) and cytidine (C*) sugar modifications and calculated their sugar conformational parameters. We also calculated the Watson-Crick hydrogen bond energies of the modified RNA-type base pairs (U*:A and C*:G) using DFT and sSAPT0 methods. The W-C base pairing energy calculations suggested that the South-type modified sugar strengthens the C*:G base pair and weakens the U*:A base pair compared to the unmodified one. In contrast, the North-type sugar modifications form weaker C*:G base pair and marginally stronger U*:A base pair compared to the South-type modified sugars. Moreover, intrastrand base stacking energies were calculated for 15 modifications incorporated at the fourth position in 7-mer non-self-complementary RNA duplexes [(GCAU*GAC)2 and (GCAC*GAC)2], utilizing molecular dynamics simulation and quantum mechanical (DFT and sSAPT0) methods. The sugar modifications were found to have minimal effect on the intrastrand base-stacking interactions. However, the glycol nucleic acid modification disturbs the intrastrand base-stacking significantly, corroborating the experimental data.