The GAMESS-UK electronic structure package: algorithms, developments and applications

CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed

Since its inception nearly a half century ago, CHARMM has been playing a central role in computational biochemistry and biophysics. Commensurate with the developments in experimental research and advances in computer hardware, the range of methods and applicability of CHARMM have also grown. This review summarizes major developments that occurred after 2009 when the last review of CHARMM was published. They include the following: new faster simulation engines, accessible user interfaces for convenient workflows, and a vast array of simulation and analysis methods that encompass quantum mechanical, atomistic, and coarse-grained levels, as well as extensive coverage of force fields. In addition to providing the current snapshot of the CHARMM development, this review may serve as a starting point for exploring relevant theories and computational methods for tackling contemporary and emerging problems in biomolecular systems. CHARMM is freely available for academic and nonprofit research at https://academiccharmm.org/program.

The ultraviolet and vacuum ultraviolet absorption spectrum of gamma-pyrone; the singlet states studied by configuration interaction and density functional calculations

A synchrotron based vacuum ultraviolet absorption spectrum for γ-pyrone has been interpreted in terms of singlet excited electronic states using a variety of coupled cluster, configuration interaction, and density functional calculations. The extremely weak spectral onset at 3.557 eV shows eight vibrational peaks, which following previous analyses, are attributed to a forbidden 1A2 state. A contrasting broad peak with a maximum at 5.381 eV has a relatively high cross-section of 30 Mb; this arises from three overlapping states, where a 1A1 state dominates over progressively weaker 1B2 and 1B1 states. After fitting the second band to a polynomial Gaussian function and plotting the regular residuals over 20 vibrational peaks, we have had limited success in analyzing this fine structure. However, the small separation between these three states clearly shows that their vibrational satellites must overlap. Singlet valence and Rydberg state vibrational profiles were determined by configuration interaction using the CAM-B3LYP density functional. Vibrational analysis using both the Franck-Condon and Herzberg-Teller procedures showed that both procedures contributed to the profiles. Theoretical Rydberg states were evaluated by a highly focused CI procedure. The superposition of the lowest photoelectron spectral band on the vacuum ultraviolet spectrum near 6.4 eV shows that the 3s and 3p Rydberg states based on the 2B2 ionic state are present; those based on the other low-lying ionic state (X2B1) are destroyed by broadening; this is a dramatic extension of the broadening previously witnessed in our studies of halogenobenzenes.

Changes in aromaticity of spin-crossover complexes: a signature for non-innocent ligands

The influence of the spin state of the metal centre in spin crossover compounds on the aromaticity of the ligands has been investigated for iron(II)tris-bipyridine (Fe(bpy)32+), and Fe(II)(formazanate)2 (as a truncated model and the full phenyl substituted compound). It was found that the aromaticity of the bipyridine ligands is unaffected by changing the spin state of the central iron atom, but that of the formazanate ligands is reduced upon transition to the high-spin state. This change in aromaticity is rationalized using the symmetry selection rules for aromaticity in terms of virtual excitations from occupied to empty orbitals. A further consequence of this loss in aromaticity is a shift to higher energy in the ring vibrations of the formazanate compounds that can be observed in either its IR or Raman spectrum; this prediction has been confirmed here. This change in aromaticity as a consequence of change in spin state can be regarded as an indication for non-innocent ligands.

The Challenging World of Simple Inorganic Rings: Revisiting Roesky's Ketone and Roesky's Sulfoxide

The surprising differences between the experimental solid-state and calculated gas-phase structures of 5-oxo-1,3,2,4-dithiadiazole (Roesky's ketone, 1) and 1-oxo-1,2,4,3,5-trithiadiazole (Roesky's sulfoxide, 2), identified and studied in a series of papers published between 2004 and 2010 but then never satisfactorily explained, have been revisited, making use of the more advanced computational possibilities currently available. The previous calculations' considerable overestimations of the C-S and S-S bond lengths in 1 and 2, respectively, have been partly explained based on the results of periodic calculations and the application of Valence Bond (VB) Theory. In the case of 1, the crystal environment appears to stabilize a structure with a highly polarized C=O bond, which features a C-S bond with considerable double-bond character - an effect which does not exist for the isolated molecule - explaining the much shorter bond in the solid state. For 2, a similar conclusion can be drawn for the S-S distance. For both compounds, though, packing effects are not the sole source of the differences: the inability of Density Functional Theory (DFT) to properly deal with the electronic structures of these apparently simple main-group systems remains a contributing factor.

Effects of L-ascorbic acid (C6H8O6: Vit-C) on collagen amino acids: DFT study

Vitamin C plays a very important role in the repair of connective tissue, especially for sports whose training causes the most damage to this tissue. Therefore, many people believe that L-ascorbic acid (C6H8O6: vitamin C) reduces the recovery time between sports exercises. The most abundant form of structural protein in the body is collagen. Collagen is characterized by a high concentration of the three amino acids glycine (Gly), proline (Pro), and hydroxyproline (Hyp), which creates its characteristic triple helix structure. Therefore, in this study, the effect of vitamin C presence on the sequence, interaction, and orientation of amino acids for collagen formation is investigated using computational simulation. This study aimed to investigate the mechanism of action of vitamin C in terms of thermodynamics and structure of the reaction. The calculations are performed using density function theory (DFT) by the base set of B3LYP/6-311++G (p,d). The results show that the presence of vitamin C is effective in the formation of collagen protein for this interaction and the mechanism of amino acid sequence (Gly-Hyp-Pro) is better in the formation of collagen protein in the presence of vitamin C. The presence of Vit-C in the formation and direction of hydroxyproline (Hyp) causes its separation from the prolyl 5-hydroxylase enzyme. In the absence of vitamin C, the reaction stops at this stage and proline cannot be converted into hydroxyproline. The computational data shows vitamin C prevents unwanted interactions and directs amino acid reactions to repair connective tissue (collagen). Therefore, vitamin C acts as a cofactor in the Prolyl 5-Hydroxylase enzyme and causes it to convert proline to hydroxyl.

Towards universal synthetic heterotrophy using a metabolic coordinator

Engineering the utilization of non-native substrates, or synthetic heterotrophy, in proven industrial microbes such as Saccharomyces cerevisiae represents an opportunity to valorize plentiful and renewable sources of carbon and energy as inputs to bioprocesses. We previously demonstrated that activation of the galactose (GAL) regulon, a regulatory structure used by this yeast to coordinate substrate utilization with biomass formation during growth on galactose, during growth on the non-native substrate xylose results in a vastly altered gene expression profile and faster growth compared with constitutive overexpression of the same heterologous catabolic pathway. However, this effort involved the creation of a xylose-inducible variant of Gal3p (Gal3pSyn4.1), the sensor protein of the GAL regulon, preventing this semi-synthetic regulon approach from being easily adapted to additional non-native substrates. Here, we report the construction of a variant Gal3pMC (metabolic coordinator) that exhibits robust GAL regulon activation in the presence of structurally diverse substrates and recapitulates the dynamics of the native system. Multiple molecular modeling studies suggest that Gal3pMC occupies conformational states corresponding to galactose-bound Gal3p in an inducer-independent manner. Using Gal3pMC to test a regulon approach to the assimilation of the non-native lignocellulosic sugars xylose, arabinose, and cellobiose yields higher growth rates and final cell densities when compared with a constitutive overexpression of the same set of catabolic genes. The subsequent demonstration of rapid and complete co-utilization of all three non-native substrates suggests that Gal3pMC-mediated dynamic global gene expression changes by GAL regulon activation may be universally beneficial for engineering synthetic heterotrophy.

Multiscale QM/MM modelling of catalytic systems with ChemShell

Hybrid quantum mechanical/molecular mechanical (QM/MM) methods are a powerful computational tool for the investigation of all forms of catalysis, as they allow for an accurate description of reactions occurring at catalytic sites in the context of a complicated electrostatic environment. The scriptable computational chemistry environment ChemShell is a leading software package for QM/MM calculations, providing a flexible, high performance framework for modelling both biomolecular and materials catalysis. We present an overview of recent applications of ChemShell to problems in catalysis and review new functionality introduced into the redeveloped Python-based version of ChemShell to support catalytic modelling. These include a fully guided workflow for biomolecular QM/MM modelling, starting from an experimental structure, a periodic QM/MM embedding scheme to support modelling of metallic materials, and a comprehensive set of tutorials for biomolecular and materials modelling.

Computational infrared and Raman spectra by hybrid QM/MM techniques: a study on molecular and catalytic material systems

Vibrational spectroscopy is one of the most well-established and important techniques for characterizing chemical systems. To aid the interpretation of experimental infrared and Raman spectra, we report on recent theoretical developments in the ChemShell computational chemistry environment for modelling vibrational signatures. The hybrid quantum mechanical and molecular mechanical approach is employed, using density functional theory for the electronic structure calculations and classical forcefields for the environment. Computational vibrational intensities at chemical active sites are reported using electrostatic and fully polarizable embedding environments to achieve more realistic vibrational signatures for materials and molecular systems, including solvated molecules, proteins, zeolites and metal oxide surfaces, providing useful insight into the effect of the chemical environment on the signatures obtained from experiment. This work has been enabled by the efficient task-farming parallelism implemented in ChemShell for high-performance computing platforms.  This article is part of a discussion meeting issue 'Supercomputing simulations of advanced materials'.

Stability Constant and Potentiometric Sensitivity of Heavy Metal-Organic Fluorescent Compound Complexes: QSPR Models for Prediction and Design of Novel Coumarin-like Ligands

Industrial wastewater often consists of toxic chemicals and pollutants, which are extremely harmful to the environment. Heavy metals are toxic chemicals and considered one of the major hazards to the aquatic ecosystem. Analytical techniques, such as potentiometric methods, are some of the methods to detect heavy metals in wastewaters. In this work, the quantitative structure-property relationship (QSPR) was applied using a range of machine learning techniques to predict the stability constant (logβ_ML) and potentiometric sensitivity (PS_ML) of 200 ligands in complexes with the heavy metal ions Cu²⁺, Cd²⁺, and Pb²⁺. In result, the logβML models developed for four ions showed good performance with square correlation coefficients (R²) ranging from 0.80 to 1.00 for the training and 0.72 to 0.85 for the test sets. Likewise, the PSML displayed acceptable performance with an R² of 0.87 to 1.00 for the training and 0.73 to 0.95 for the test sets. By screening a virtual database of coumarin-like structures, several new ligands bearing the coumarin moiety were identified. Three of them, namely NEW02, NEW03, and NEW07, showed very good sensitivity and stability in the metal complexes. Subsequent quantum-chemical calculations, as well as physicochemical/toxicological profiling were performed to investigate their metal-binding ability and developability of the designed sensors. Finally, synthesis schemes are proposed to obtain these three ligands with major efficiency from simple resources. The three coumarins designed clearly demonstrated capability to be suitable as good florescent chemosensors towards heavy metals. Overall, the computational methods applied in this study showed a very good performance as useful tools for designing novel fluorescent probes and assessing their sensing abilities.

Extracting Quantitative Information at Quantum Mechanical Level from Noncovalent Interaction Index Analyses

The noncovalent interaction (NCI) index is nowadays a well-known strategy to detect NCIs in molecular systems. Even though it initially provided only qualitative descriptions, the technique has been recently extended to also extract quantitative information. To accomplish this task, integrals of powers of the electron distribution were considered, with the requirement that the overall electron density can be clearly decomposed as sum of distinct fragment contributions to enable the definition of the (noncovalent) integration region. So far, this was done by only exploiting approximate promolecular electron densities, which are given by the sum of spherically averaged atomic electron distributions and thus represent too crude approximations. Therefore, to obtain more quantum mechanically (QM) rigorous results from NCI index analyses, in this work, we propose to use electron densities obtained through the transfer of extremely localized molecular orbitals (ELMOs) or through the recently developed QM/ELMO embedding technique. Although still approximate, the electron distributions resulting from the abovementioned methods are fully QM and, above all, are again partitionable into subunit contributions, which makes them completely suitable for the NCI integral approach. Therefore, we benchmarked the integrals resulting from NCI index analyses (both those based on the promolecular densities and those based on ELMO electron distributions) against interaction energies computed at a high quantum chemical level (in particular, at the coupled cluster level). The performed test calculations have indicated that the NCI integrals based on ELMO electron densities outperform the promolecular ones. Furthermore, it was observed that the novel quantitative NCI-(QM/)ELMO approach can be also profitably exploited both to characterize and evaluate the strength of specific interactions between ligand subunits and protein residues in protein-ligand complexes and to follow the evolution of NCIs along trajectories of molecular dynamics simulations. Although further methodological improvements are still possible, the new quantitative ELMO-based technique could be already exploited in situations in which fast and reliable assessments of NCIs are crucial, such as in computational high-throughput screenings for drug discovery.

Photo-ionization initiated differential ultrafast charge migration: impacts of molecular symmetries and tautomeric forms

Photo-ionization induced ultrafast electron dynamics is considered as a precursor for the slower nuclear dynamics associated with molecular dissociation. Here, using the ab initio multielectron wave-packet propagation method, we study the overall many-electron dynamics, triggered by ionizing the outer-valence orbitals of different tautomers for a prototype molecule with more than one symmetry element. From the time evolution of the initially created averaged hole density of each system, we identify distinctly different charge dynamics responses in the tautomers. We observe that the keto form shows a charge migration direction away from the nitrogen bonded with hydrogen, while in enol-U - away from oxygen bonded to hydrogen. Additionally, the dynamics following the ionization of molecular orbitals with different symmetries reveals that a' orbitals show a fast and highly delocalized charge density in comparison to a'' symmetry. These observations indicate why different tautomers respond differently to an XUV ionization, and might explain the subsequent different fragmentation pathways. An experimental schematics allowing the detection and reconstruction of such charge dynamics is also proposed. Although the present study uses a simple, prototypical bio-relevant molecule, it reveals the explicit role of molecular symmetry and tautomerism in the ionization-triggered charge migration that controls many ultrafast physical, chemical, and biological processes, making tautomeric forms a promising tool of molecular design for desired charge migration.

Current Trends and Changes in Use of Membrane Molecular Dynamics Simulations within Academia and the Pharmaceutical Industry

There has been an almost exponential increase in the use of molecular dynamics simulations in basic research and industry over the last 5 years, with almost a doubling in the number of publications each year. Many of these are focused on neurological membranes, and biological membranes in general, applied to the medical industry. A smaller portion have utilized membrane simulations to answer more basic questions related to the function of specific proteins, chemicals or biological processes. This review covers some newer studies, alongside studies from the last two decades, to determine changes in the field. Some of these are basic, while others are more profound, such as multi-component embedded membrane machinery. It is clear that many facets of the discipline remain the same, while the focus on and uses of the technology are broadening in scope and utilization as a general research tool. Analysis of recent literature provides an overview of the current methodologies, covers some of the recent trends or advances and tries to make predictions of the overall path membrane molecular dynamics will follow in the coming years. In general, the overview presented is geared towards the general scientific community, who may wish to introduce the use of these methodologies in light of these changes, making molecular dynamic simulations more feasible for general scientific or medical research.

The Halogen Bond in Weakly Bonded Complexes and the Consequences for Aromaticity and Spin-Orbit Coupling

The halogen bond complexes CF3X⋯Y and C2F3X⋯Y, with Y = furan, thiophene, selenophene and X = Cl, Br, I, have been studied by using DFT and CCSD(T) in order to understand which factors govern the interaction between the halogen atom X and the aromatic ring. We found that PBE0-dDsC/QZ4P gives an adequate description of the interaction energies in these complexes, compared to CCSD(T) and experimental results. The interaction between the halogen atom X and the π-bonds in perpendicular orientation is stronger than the interaction with the in-plane lone pairs of the heteroatom of the aromatic cycle. The strength of the interaction follows the trend Cl < Br < I; the chalcogenide in the aromatic ring nor the hybridization of the C−X bond play a decisive role. The energy decomposition analysis shows that the interaction energy is dominated by all three contributions, viz., the electrostatic, orbital, and dispersion interactions: not one factor dominates the interaction energy. The aromaticity of the ring is undisturbed upon halogen bond formation: the π-ring current remains equally strong and diatropic in the complex as it is for the free aromatic ring. However, the spin-orbit coupling between the singlet and triplet π→π* states is increased upon halogen bond formation and a faster intersystem crossing between these states is therefore expected.

The ionic and ground states of gamma-pyrone. The photoionization spectrum studied by synchrotron radiation and interpreted by configuration interaction and density functional calculations

A synchrotron-based photoionization spectrum up to 27 eV represents a considerable improvement in resolution over early He(I) and He(II) spectra. Symmetry-adapted coupled cluster calculations of the ionic state sequence give the sequence of state vertical ionization energies (VIE) as 1²B₂ < 1²B₁ < 1²A₂ < 2²B₁ < 1²A₁. Generally, these symmetry-adapted cluster configuration interactions VIE match reasonably well with the experimental spectrum over this wide energy range. Density functional calculations of the corresponding adiabatic terms (AIE) were also performed. Higher energy ionic states were determined by complete active space self-consistent field methods; these include all π-ionizations and some σ-ionic states. These were analyzed by Franck-Condon (FC) procedures and compared with an experiment. The spectral onset is complex, where two states, later shown to be the 1²B₂ and 1²B₁ states, are strongly overlapping. The superposition of the FC vibrational structure in the 1²B₂ and 1²B₁ states accounts for most of the peaks arising at the onset of the photoelectron spectra. However, the small separation between these two ionic states makes vibronic interaction fairly inevitable. In the absence of Herzberg-Teller analyses for ionic states, we have sought and determined a transition state between the 1²B₂ and 1²B₁ states, showing that vibronic coupling does occur. The lack of degradation in the vibrational envelope of the higher of the two states contrasts with our previous work on the halogenobenzenes, where overlapping state envelopes led to considerable widening of the line width at half-height of the higher energy states.

Initial Maximum Overlap Method Embedded with Extremely Localized Molecular Orbitals for Core-Ionized States of Large Systems

Despite great advances in X-ray absorption spectroscopy for the investigation of small molecule electronic structure, the application to biosystems of experimental techniques developed within this research field remains a challenge. To partially circumvent the problem, users resort to theoretical methods to interpret or predict the X-ray absorption spectra of large molecules. To accomplish this task, only low-cost computational strategies can be exploited. For this reason, some of them are single Slater determinant wavefunction approaches coupled with multiscale embedding techniques designed to treat large systems of biological interest. Therefore, in this work, we propose to apply the recently developed IMOM/ELMO embedding method to the determination of core-ionized states. The IMOM/ELMO technique resulted from the combination of the single Slater determinant Δself-consistent-field-initial maximum overlap approach (ΔSCF-IMOM) with the QM/ELMO (quantum mechanics/extremely localized molecular orbital) embedding strategy, a method where only the chemically relevant region of the examined system is treated at fully quantum chemical level, while the rest is described through transferred and frozen extremely localized molecular orbitals (ELMOs). The IMOM/ELMO technique was initially validated by computing core-ionization energies for small molecules, and it was afterwards exploited to study larger biosystems. The obtained results are in line with those reported in previous studies that applied alternative ΔSCF approaches. This makes us envisage a possible future application of the proposed method to the interpretation of X-ray absorption spectra of large molecules.

Influence of Solvent on Selective Catalytic Reduction of Nitrogen Oxides with Ammonia over Cu-CHA Zeolite

The copper-exchanged zeolite Cu-CHA has received considerable attention in recent years, owing to its application in the selective catalytic reduction (SCR) of NO_x species. Here, we study the NH₃-SCR reaction mechanism on Cu-CHA using the hybrid quantum mechanical/molecular mechanical (QM/MM) technique and investigate the effects of solvent on the reactivity of active Cu species. To this end, a comparison is made between water- and ammonia-solvated and bare Cu species. The results show the promoting effect of solvent on the oxidation component of the NH₃-SCR cycle since the formation of important nitrate species is found to be energetically more favorable on the solvated Cu sites than in the absence of solvent molecules. Conversely, both solvent molecules are predicted to inhibit the reduction component of the NH₃-SCR cycle. Diffuse reflectance infrared fourier-transform spectroscopy (DRIFTS) experiments exploiting (concentration) modulation excitation spectroscopy (MES) and phase-sensitive detection (PSD) identified spectroscopic signatures of Cu-nitrate and Cu-nitrosamine (H₂NNO), important species which had not been previously observed experimentally. This is further supported by the QM/MM-calculated harmonic vibrational analysis. Additional insights are provided into the reactivity of solvated active sites and the formation of key intermediates including their formation energies and vibrational spectroscopic signatures, allowing the development of a detailed understanding of the reaction mechanism. We demonstrate the role of solvated active sites and their influence on the energetics of important species that must be explicitly considered for an accurate understanding of NH₃-SCR kinetics.

Modelling structural properties of cyanine dye nanotubes at coarse-grained level

Self-assembly is a ubiquitous process spanning from biomolecular aggregates to nanomaterials. Even though the resulting aggregates can be studied through experimental techniques, the dynamic pathways of the process and the molecular details of the final structures are not necessarily easy to resolve. Consequently, rational design of self-assembling aggregates and their properties remains extremely challenging. At the same time, modelling the self-assembly with computational methods is not trivial, because its spatio-temporal scales are usually beyond the limits of all-atom based simulations. The use of coarse-grained (CG) models can alleviate this limitation, but usually suffers from the lack of optimised parameters for the molecular constituents. In this work, we describe the procedure of parametrizing a CG Martini model for a cyanine dye (C8S3) that self-assembles into hollow double-walled nanotubes. First, we optimised the model based on quantum mechanics calculations and all-atom reference simulations, in combination with available experimental data. Then, we conducted random self-assembly simulations, and the performance of our model was tested on preformed assemblies. Our simulations provide information on the time-dependent local arrangement of this cyanine dye, when aggregates are being formed. Furthermore, we provide guidelines for designing and optimising parameters for similar self-assembling nanomaterials.

Confined helium, density dependence of the inelastic electron and photon scattering cross-sections and the optical oscillator strength

The electron and photon excitation of confined and compressed atoms is discussed. It is shown that the optical oscillator strength, the inelastic X-ray and electron impact cross-sections are all density-dependent. Ab-initio electronic structure calculations are presented for the 1 s 2 → 1 s 2 p ( 1 P ) transition in helium, which predict that the amplitudes for the inelastic scattering of electrons, optical absorption and the excitation energy are all significantly increased in bulk condensed phases of pure helium compared to those of an isolated atom. The enhancements increase with atomic density but are very similar for bcc and fcc structured bulk phases of the same density. These enhancements need to be incorporated into the analysis of scanning transmission electron microscope studies of helium nano bubbles embedded in different materials. The excitation energy and cross-section enhancements with increasing density arise from the contraction of the 2 p orbital on entering a condensed phase. For the bulk phases, but not the bubbles, the close agreement between the experimental and computed values of the energy shifts can be well described by a simple relationship.

The Interplay of Interstitial and Substitutional Copper in Zinc Oxide

Cu impurities are reported to have significant effects on the electrical and optical properties of bulk ZnO. In this work, we study the defect properties of Cu in ZnO using hybrid quantum mechanical/molecular mechanical (QM/MM)–embedded cluster calculations based on a multi-region approach that allows us to model defects at the true dilute limit, with polarization effects described in an accurate and consistent manner. We compute the electronic structure, energetics, and geometries of Cu impurities, including substitutional and interstitial configurations, and analyze their effects on the electronic structure. Under ambient conditions, Cu_Zn is the dominant defect in the d⁹ state and remains electronically passive. We find that, however, as we approach typical vacuum conditions, the interstitial Cu defect becomes significant and can act as an electron trap.

Environmental modifications of atomic properties: The ground and 1s2p excited states of compressed helium

Atoms remaining as recognizably distinct constituents of bulk condensed phases can have properties modified from those of the isolated species. Dense helium bubbles at high pressures are a common form of radiation damage degrading the mechanical and electrical properties of host materials. Detailed knowledge is critical for predicting their long term performance. Modifications of the ground and first singlet excited states of confined compressed helium are investigated using an entirely non-empirical theory based on the results of ab initio self-consistent field calculations with corrections for the effects of electron correlation. For finite sized portions representing bulk condensed fcc and bcc phases of helium atoms, Hartree-Fock wavefunctions, energies, and charge distributions were computed as a function of different atomic densities using two models. The first model for the first excited state localizes the excitation on the central atom; in the second model, this is partially delocalized over the closest atomic neighbors. Total energies for the finite size portions are derived by adding the inter-atomic dispersive attractions and a density functional description of the short-range inter-atomic correlation energy. The experimental energy of the first allowed electronic transition increases with density being larger than in an isolated atom. The intra-atomic correlation energy does not contribute to this energy shift. The calculated energy shifts agree well with experiment for both bulk solid and liquid helium. The 2p orbital is increasingly compressed by density enhancement, thus generating the energy shifts. Consequently, calculations of the inelastic electron scattering cross sections are substantially incorrect if the compression of the final 1s2p state is not included. The character of the excitations is examined, and it is argued that these are of Frenkel rather than the Wannier type.

Multidimensional Free Energy and Accelerated Quantum Library Methods Provide a Gateway to Glycoenzyme Conformational, Electronic, and Reaction Mechanisms

Enzyme reactions are complex to simulate accurately, and none more so than glycoenzymes (glycosyltransferase and glycosidases). A rigorous sampling of the protein frame and the conformationally plural carbohydrate substrate coupled with an unbiased treatment of the electron dynamics is needed to discover the true reaction landscapes. Here, we demonstrate the effectiveness of two computational methods ported in libraries that we have developed. The first is a flat histogram free energy method called FEARCF capable of multidimensional sampling and rapidly converging to a complete coverage of phase space. The second, the Quantum Supercharger Library (QSL), is a method that accelerates the computation of the ab initio electronic wave function as well as the integral derivatives on graphical processing units (GPUs). These QSL accelerated computations form the core components needed for direct quantum dynamics and QM/MM dynamics when coupled with legacy codes such as GAMESS and NWCHEM, making state of the art hyper-parallel electronic computations in chemistry and chemical biology possible. The combination of QSL (acceleration of ab initio QM computation) and FEARCF (multidimensional hyper-parallel reaction dynamics) makes the simulation of ab initio QM/MM reaction dynamics of enzyme catalysis feasible. Enzymes that process carbohydrates pose an added challenge as their pyranose ring substrates span multidimensional conformational space whose sampling is an intimate function of the catalytic mechanism. Here, we use the pairing of FEARCF and QSL to simulate the catalytic effect of the glycoenzyme β-N-acetylglucosamine transferase (OGT). The reaction mechanism is discovered from a variable three bond reaction surface using SCCDFTB. The role of the OGT in distorting the pyranose ring of β-N-acetylglucosamine (GlcNAc) away from the equilibrium 4C1 chair conformation toward the E3 envelope needed for the transition state is discovered from its pucker free energy hypersurfaces (or free energy volume, FEV). A complete GlcNAc ring pucker HF 6-31g FEV is constructed from ab initio QM dynamics in vacuum and ab initio QM/MM dynamics in the OGT catalytic domain. The OGT is shown to clearly lower the pathway toward the transition state E3 ring conformer as well as stabilize it by 1.63 kcal/mol. Illustrated here is the use of QSL accelerated ab initio QM/MM dynamics that thoroughly explores carbohydrate catalyzed reactions through a FEARCF multidimensional sampling of the interdependence between reaction and conformational space. This demonstrates how experimentally inaccessible molecular and electronic mechanisms that underpin enzyme catalysis can be discovered by directly modeling the dynamics of these complex reactions.

QM/MM study of the reactivity of zeolite bound methoxy and carbene groups

The conversion of methanol-to-hydrocarbons (MTH) is known to occur via an autocatalytic process in zeolites, where framework-bound methoxy species play a pivotal role, especially during catalyst induction. Recent NMR and FT-IR experimental studies suggest that methoxylated zeolites are able to produce hydrocarbons by a mechanism involving carbene migration and association. In order to understand these observations, we have performed QM/MM computational investigations on a range of reaction mechanisms for the reaction of zeolite bound methoxy and carbene groups, which are proposed to initiate hydrocarbon formation in the MTH process. Our simulations demonstrate that it is kinetically unfavourable for methyl species to form on the framework away from the zeolite acid site, and both kinetically and thermodynamically unfavourable for methyl groups to migrate through the framework and aggregate around an acid site. Formation of carbene moieties was considered as an alternative pathway to the formation of C-C bonds; however, the reaction energy for conversion of a methyl to a carbene is unfavourable. Metadynamics simulations help confirm further that methyl species at the framework acid sites would be more reactive towards formed C₂₊ species, rather than inter-framework migration, and that the role of carbenes in the formation of the first C-C bond will be via a concerted type of mechanism rather than stepwise.

Periodoannulenes: A Generalized Annulene-within-an-Annulene Paradigm for Combined σ and π Ring Currents

Periodoannulene molecules and ions C_xI_x^q in planar geometry offer examples of systems with the potential for outer σ and inner π ring-current double aromaticity, given a sufficient overlap of tangential p_σ-orbital manifolds on the large atoms of the outer cycle. Previous theoretical work indicated concentric diatropic currents in the dication C₆I₆²⁺. Ab initio ipsocentric calculations support an account in terms of frontier-orbital selection rules for current contributions in C₆I₆²⁺ (and radical C₆I₆⁺, implicated in recent experimental work on the oxidation of periodobenzene). A σ/π analogue of the annulene-within-an-annulene model is applied here to periodo systems based on cyclooctatetraene. Model species C₈I₈^q with charges q = 0, +1, +2, +4, -2 and structures constrained to a planar D_4h symmetry exhibit maps with all combinations of σ/π con- and counter-rotation, comprising global σ ring currents on the iodine perimeter and central π ring currents on the carbocycle. All can be rationalized by the separate application of the tropicity selection rules to the two subsystems, whether in singlet or triplet states.

The vacuum ultraviolet absorption spectrum of norbornadiene: Vibrational analysis of the singlet and triplet valence states of norbornadiene by configuration interaction and density functional calculations

A synchrotron-based vacuum ultraviolet (VUV) absorption spectrum of norbornadiene (NBD) is reported, and the extensive vibrational structure obtained has been analyzed. The previously known 5b₁3s-Rydberg state has been reinterpreted by comparison with our recent high-resolution photoelectron spectral analysis of the X²B₁ ionic state. Additional vibrational details in the region of this Rydberg state are observed in its VUV spectrum when compared with the photoelectron ²B₁ ionic state; this is attributed to the underlying valence state structure in the VUV. Valence and Rydberg state energies have been obtained by configuration interaction and time-dependent density functional theoretical methods. Several low-lying singlet valence states, especially those that arise from ππ* excitations, conventionally termed NV₁ to NV₄, have been examined in detail. Their Franck-Condon (FC) and Herzberg-Teller (HT) profiles have been investigated and fitted to the VUV spectrum. Estimates of the experimental 0⁰ band positions have been made from these fits. The anomaly of the observed UV absorption by the ¹A₂ state of NBD is attributed to HT effects. Generally, the HT components are less than 10% of the FC terms. The calculated 5b₁3s lowest Rydberg state also shows a low level of HT components. The observed electron impact spectra of NBD have been analyzed in detail in terms of triplet states.

Initial Maximum Overlap Method for Large Systems by the Quantum Mechanics/Extremely Localized Molecular Orbital Embedding Technique

Quantum chemistry offers a large variety of methods to treat excited states. Many of them are based on a multireference wave function ansatz and are therefore characterized by an intrinsic complexity and high computational costs. To overcome these drawbacks and also some limitations of simpler single-reference approaches (e.g., configuration interaction singles and time-dependent density functional theory), the single-determinant Δself-consistent field-initial maximum overlap method (ΔSCF-IMOM) has been proposed. This strategy substitutes the aufbau principle with a criterion that occupies molecular orbitals at successive SCF iterations on the basis of their maximum overlap with a proper set of guess orbitals for the target excited state. In this way, it prevents the SCF process to collapse to the ground state wave function and provides excited state single Slater determinant solutions to the SCF equations. Here, we propose to extend the applicability of the IMOM to the treatment of localized excited states of large systems. To accomplish this task, we coupled it with the QM/ELMO (quantum mechanics/extremely localized molecular orbitals) strategy, a quantum mechanical embedding method in which the most chemically relevant part of the system is treated with traditional quantum chemical approaches, while the rest is described by extremely localized molecular orbitals transferred from recently constructed libraries or proper model molecules. After presenting the theoretical foundations of the new IMOM/ELMO technique, in this paper, we will show and discuss the results of preliminary test calculations carried out on both model systems (i.e., decanoic acid, decene, decapentaene, and solvated acrolein) and a system of biological interest (flavin mononucleotide in the flavodoxin protein). We observed that, for localized excited states, the new IMOM/ELMO method provides reliable results, and it reproduces the outcomes of fully IMOM calculations within the chemical accuracy threshold (i.e., 0.043 eV) by including only a limited number of atoms in the QM region. Furthermore, the first application of our embedding technique to a larger biological system gave completely plausible results in line with those obtained through more traditional quantum mechanical methods, thus opening the possibility of using the new approach in future investigations of photobiology problems.

Three-Layer Multiscale Approach Based on Extremely Localized Molecular Orbitals to Investigate Enzyme Reactions

Quantum mechanics/molecular mechanics (QM/MM) calculations are widely used embedding techniques to computationally investigate enzyme reactions. In most QM/MM computations, the quantum mechanical region is treated through density functional theory (DFT), which offers the best compromise between chemical accuracy and computational cost. Nevertheless, to obtain more accurate results, one should resort to wave function-based methods, which however lead to a much larger computational cost already for relatively small QM subsystems. To overcome this drawback, we propose the coupling of our QM/ELMO (quantum mechanics/extremely localized molecular orbital) approach with molecular mechanics, thus introducing the three-layer QM/ELMO/MM technique. The QM/ELMO strategy is an embedding method in which the chemically relevant part of the system is treated at the quantum mechanical level, while the rest is described through frozen ELMOs. Since the QM/ELMO method reproduces results of fully QM computations within chemical accuracy and with a much lower computational effort, it can be considered a suitable strategy to extend the range of applicability and accuracy of the QM/MM scheme. In this paper, other than briefly presenting the theoretical bases of the QM/ELMO/MM technique, we will also discuss its validation on the well-tested deprotonation of acetyl coenzyme A by aspartate in citrate synthase.

Ionic bond in hydrogen transferring of the ferrous and/or ferric human/mouse verdoheme oxygenase

Formation of five coordinated ferric (ferrous) verdoheme oxygenase complexes have been investigated at ωB97X-D/6-31G(d) level of theory. This process was carried out by adsorption of imidazole and human/mouse verdoheme oxygenase (VO) compounds. Global reactivity indexes show electrophile and nucleophile roles of the VO complexes and Imidazole, respectively. This result confirms their interaction, molecular electrostatic potential (MEP) maps, and low HOMO_FRVMO-LUMO_Imidazole gap. These interactions can cause in adsorption and five coordinated of the VO complexes. More negative value (-64.3 kJ mol^-1) of adsorption energy (E_ads) in the FRVMO complex shows better adsorption strength and stable configuration. Significant point of this interaction is hydrogen transfer from imidazole to the nearest oxygen of the VO complexes; this issue is approved using quantum theory of atom in molecule (QTAIM) and natural bond orbital (NBO) analysis. QTAIM calculations confirm ionic bonding between the transferred hydrogen and the oxygen atom of the VO. The 312.2-kcal mol^-1 s order stabilization energies in this complex are confirmation for strong donation and better formation of five coordinated complex in electron view point.

From NWChem to NWChemEx: Evolving with the Computational Chemistry Landscape

Since the advent of the first computers, chemists have been at the forefront of using computers to understand and solve complex chemical problems. As the hardware and software have evolved, so have the theoretical and computational chemistry methods and algorithms. Parallel computers clearly changed the common computing paradigm in the late 1970s and 80s, and the field has again seen a paradigm shift with the advent of graphical processing units. This review explores the challenges and some of the solutions in transforming software from the terascale to the petascale and now to the upcoming exascale computers. While discussing the field in general, NWChem and its redesign, NWChemEx, will be highlighted as one of the early codesign projects to take advantage of massively parallel computers and emerging software standards to enable large scientific challenges to be tackled.

Electronic couplings for singlet fission: Orbital choice and extrapolation to the complete basis set limit

For the search for promising singlet fission candidates, the calculation of the effective electronic coupling, which is required to estimate the singlet fission rate between the initially excited state (S0S1) and the multiexcitonic state (1TT, two triplets on neighboring molecules, coupled into a singlet), should be sufficiently reliable and fast enough to explore the configuration space. We propose here to modify the calculation of the effective electronic coupling using a nonorthogonal configuration interaction approach by: (a) using only one set of orbitals, optimized for the triplet state of the molecules, to describe all molecular electronic states, and (b) only taking the leading configurations into consideration. Furthermore, we also studied the basis set convergence of the electronic coupling, and we found, by comparison to the complete basis set limit obtained using the cc-pVnZ series of basis sets, that both the aug-cc-pVDZ and 6-311++G** basis sets are a good compromise between accuracy and computational feasibility. The proposed approach enables future work on larger clusters of molecules than dimers.

QM/MM study of the stability of dimethyl ether in zeolites H-ZSM-5 and H-Y

The methanol-to-hydrocarbons (MTH) process transforms C1 carbon sources to higher hydrocarbons, but details of the mechanism that leads to the formation of the first carbon-carbon bond remain unclear. Here, we present a computational investigation of how a crucial intermediate, dimethyl ether (DME), interacts with different zeolite catalysts (H-ZSM-5, H-Y) to gain insight into the initial stages in the MTH process. We use QM/MM computational simulations to model the conversion of methanol to DME in H-ZSM-5, which is a well characterised and important reaction intermediate. We analyse and compare the stability of DME on several acid sites in H-ZSM-5 and H-Y, and show that the more acidic and open "intersection sites" in the H-ZSM-5 framework are able to bond strongest with DME, with complete deprotonation of the acid site occurring. The conversion of methanol to DME in H-ZSM-5 is calculated as requiring a higher activation energy than framework methoxylation, which indicates that a stepwise (indirect) mechanism, through a methoxy intermediate, is the most likely route to DME formation during the initiation of the MTH process.

The electronic structure of carbones revealed: insights from valence bond theory

In this contribution, we studied the OC-C bond in carbon suboxide and related allene compounds using the valence bond method. The nature of this bond has been the subject of debate, whether it is a regular, electron sharing bond or a dative bond. We compared the nature of this bond in carbon suboxide with the gold-CO bond in Au(CO)₂⁺, which is a typical dative bond, and we studied its charge-shift bond character. We found that the C-CO bond in carbon suboxide is unique in the sense that it cannot be assigned as either a dative or electron sharing bond, but it is an admixture of electron sharing and dative components, together with a high contribution of ionic character. These findings provide a clear basis for distinguishing the commonly found dative bonds between ligands and transition metals and the present case of what may be described as coordinative bonding to carbon.

Quantum Mechanics/Extremely Localized Molecular Orbital Embedding Strategy for Excited States: Coupling to Time-Dependent Density Functional Theory and Equation-of-Motion Coupled Cluster

The QM/ELMO (quantum mechanics/extremely localized molecular orbital) method is a recently developed embedding technique in which the most important region of the system under examination is treated at fully quantum mechanical level, while the rest is described by means of transferred and frozen extremely localized molecular orbitals. In this paper, we propose the first application of the QM/ELMO approach to the investigation of excited states, and, in particular, we present the coupling of the QM/ELMO philosophy with Time-Dependent Density Functional Theory (TDDFT) and Equation-of-Motion Coupled Cluster with single and double substitutions (EOM-CCSD). The proposed TDDFT/ELMO and EOM-CCSD/ELMO strategies underwent a series of preliminary tests that were already considered for the validation of other embedding methods for excited states. The obtained results showed that the novel techniques allow the accurate description of localized excitations in large systems by only including a relatively small number of atoms in the region treated at fully quantum chemical level. Furthermore, for TDDFT/ELMO, it was also observed that (i) the method enables to avoid the presence of artificial low-lying charge-transfer states that may affect traditional TDDFT calculations, even using functionals that do not take into account long-range corrections, and (ii) the novel approach can be also successfully exploited to investigate local electronic transitions in quite large systems (e.g., reduced model of the Green Fluorescent Protein), and the accuracy of the results can be improved by including a sufficient number of chemically crucial fragments/residues in the quantum mechanical region. Finally, concerning EOM-CCSD/ELMO, it was also seen that, despite the quite crude approximation of an embedding potential given by frozen extremely localized molecular orbitals, the new strategy is able to satisfactorily account for the effects of the environment. This work paves the way to further extensions of the QM/ELMO philosophy for the study of local excitations in extended systems, suggesting the coupling of the QM/ELMO approach with other quantum chemical strategies for excited states, from the simplest ΔSCF techniques to the most advanced and computationally expensive multireferences methods.

Structural characterization of supramolecular hollow nanotubes with atomistic simulations and SAXS

Self-assembled nanostructures arise when building blocks spontaneously organize into ordered aggregates that exhibit different properties compared to the disorganized monomers. Here, we study an amphiphilic cyanine dye (C8S3) that is known to self-assemble into double-walled, hollow, nanotubes with interesting optical properties. The molecular packing of the dyes inside the nanotubes, however, remains elusive. To reveal the structural features of the C8S3 nanotubes, we performed atomistic Molecular Dynamics simulations of preformed bilayers and nanotubes. We find that different packing arrangements lead to stable structures, in which the tails of the C8S3 molecules are interdigitated. Our results are verified by SAXS experiments. Together our data provide a detailed structural characterization of the C8S3 nanotubes. Furthermore, our approach was able to resolve the ambiguity inherent from cryo-TEM measurements in calculating the wall thickness of similar systems. The insights obtained are expected to be generally useful for understanding and designing other supramolecular assemblies.

Methanol loading dependent methoxylation in zeolite H-ZSM-5

We evaluate the effect of the number of methanol molecules per acidic site of H-ZSM-5 on the methoxylation reaction at room temperature by applying operando diffuse reflectance infrared Fourier transformed spectroscopy (DRIFTS) and mass spectrometry (MS), which capture the methoxylation reaction by simultaneously probing surface adsorbed species and reaction products, respectively. To this end, the methanol loading in H-ZSM-5 (Si/Al ≈ 25) pores is systematically varied between 32, 16, 8 and 4 molecules per unit cell, which corresponds to 8, 4, 2 and 1 molecules per Brønsted acidic site, respectively. The operando DRIFTS/MS data show that the room temperature methoxylation depends on the methanol loading: the higher the methanol loading, the faster the methoxylation. Accordingly, the reaction is more than an order of magnitude faster with 8 methanol molecules per Brønsted acidic site than that with 2 molecules, as evident from the evolution of the methyl rock band of the methoxy species and of water as a function of time. Significantly, no methoxylation is observed with ≤1 molecule per Brønsted acidic site. However, hydrogen bonded methanol occurs across all loadings studied, but the structure of hydrogen bonded methanol also depends on the loading. Methanol loading of ≤1 molecule per acidic site leads to the formation of hydrogen bonded methanol with no proton transfer (i.e. neutral geometry), while loading ≥2 molecules per acidic site results in a hydrogen bonded methanol with a net positive charge on the adduct (protonated geometry). The infrared vibrational frequencies of methoxy and hydrogen bonded methanol are corroborated by Density Functional Theory (DFT) calculations. Both the experiments and calculations reflect the methoxy bands at around 940, 1180, 2868-2876 and 2980-2973 cm-1 which correspond to ν(C-O), ρ(CH3), ν s(C-H) and ν as(C-H), respectively.

Localized Molecular Orbital-Based Embedding Scheme for Correlated Methods

Embedding strategies currently provide the best compromise between accuracy and computational cost in modeling chemical properties and processes of large and complex systems. In this framework, different methods have been proposed all over the years, from the very popular QM/MM approaches to the more recent and very promising density matrix and density functional embedding techniques. Here, we present a further development of the quantum mechanics/extremely localized molecular orbital technique (QM/ELMO) method, a recently proposed multiscale embedding strategy in which the chemically active region of the investigated system is treated at a fully quantum mechanical level, while the rest is described by frozen extremely localized molecular orbitals previously transferred from proper libraries or tailor-made model molecules. In particular, in this work we discuss and assess in detail the extension of the QM/ELMO approach to density functional theory and post-Hartree-Fock techniques by evaluating its performances when it is used to describe chemical reactions, bond dissociations, and intermolecular interactions. The preliminary test calculations have shown that, in the investigated cases, the new embedding strategy enables the results of the corresponding fully quantum mechanical computations to be reproduced within chemical accuracy in almost all the cases but with a significantly reduced computational cost, especially when correlated post-Hartree-Fock strategies are used to describe the quantum mechanical subsystem. In light of the obtained results, we already envisage the future application of the new correlated QM/ELMO techniques to the investigation of more challenging problems, such as the modeling of enzyme catalysis, the study of excited states of biomolecules, and the refinement of macromolecular X-ray crystal structures.

Reduced Common Molecular Orbital Basis for Nonorthogonal Configuration Interaction

Electron and charge transfers are part of many vital processes in nature and technology. Ab initio descriptions of these processes provide useful insights that can be utilized for applications. A combination of the embedded cluster material model and nonorthogonal configuration interaction (NOCI), in which the cluster wave functions are expanded in many-electron basis functions (MEBFs) consisting of spin-adapted, antisymmetrized products of multiconfigurational wave functions of fragments (which are usually molecules) in the cluster, appears to provide a compromise between accuracy and calculation time. Additional advantages of this NOCI-Fragments approach are the chemically convenient interpretation of the wave function in terms of molecular states, and the direct accessibility of electronic coupling between diabatic states to describe energy and electron transfer processes. Bottlenecks in this method are the large number of two-electron integrals that have to be handled for the calculation of an electronic coupling matrix element and the enormous number of matrix elements over determinant pairs that have to be evaluated for the calculation of one matrix element between the MEBFs. We show here how we created a reduced common molecular orbital basis that is utilized to significantly reduce the number of two-electron integrals that need to be handled. The results obtained with this basis do not show any loss of accuracy in relevant quantities like electronic couplings and vertical excitation energies. We also show a significant reduction in computation time without loss in accuracy when matrix elements over determinant pairs with small weights are neglected in the NOCI. These improvements in the methodology render NOCI-Fragments to be also applicable to treat clusters of larger molecular systems with larger atomic basis sets and larger active spaces, as the computation time becomes dependent on the number of occupied orbitals and less dependent on the size of the active space.

Orbital Decomposition of the Carbon Chemical Shielding Tensor in Gold(I) N-Heterocyclic Carbene Complexes

The good performance of N-heterocyclic carbenes (NHCs), in terms of versatility and selectivity, has called the attention of experimentalists and theoreticians attempting to understand their electronic properties. Analyses of the Au(I)-C bond in [(NHC)AuL]+/0 (L stands for a neutral or negatively charged ligand), through the Dewar-Chatt-Duncanson model and the charge displacement function, have revealed that NHC is not purely a σ-donor but may have a significant π-acceptor character. It turns out, however, that only the σ-donation bonding component strongly correlates with one specific component of the chemical shielding tensor. Here, in extension to earlier works, a current density analysis, based on the continuous transformation of the current density diamagnetic zero approach, along a series of [(NHC)AuL]+/0 complexes is presented. The shielding tensor is decomposed into orbital contributions using symmetry considerations together with a spectral analysis in terms of occupied to virtual orbital transitions. Analysis of the orbital transitions shows that the induced current density is largely influenced by rotational transitions. The orbital decomposition of the shielding tensor leads to a deeper understanding of the ligand effect on the magnetic response properties and the electronic structure of (NHC)-Au fragments. Such an orbital decomposition scheme may be extended to other magnetic properties and/or substrate-metal complexes.