Search

The ab initio molecular dynamics (AIMD) method provides a computational route for the real-time simulation of reactive chemistry. An often-overlooked capability of this approach is the opportunity to examine the electronic evolution of a chemical system. For AIMD trajectories based on Hartree-Fock or density functional theory methods, the real-time evolution of single-particle molecular orbitals (MOs) can provide detailed insights into the time-dependent electronic structure of molecules. The evolving electronic Hamiltonians at each MD step pose problems for tracking and visualizing a given MO's character, ordering, and associated phase throughout an MD trajectory, however. This report presents and assesses a simple algorithm for correcting these deficiencies by exploiting similarity projections of the electronic structure between neighboring MD steps. Two aspects bring this analysis beyond a simple step-to-step projection scheme. First, the challenging case of coincidental orbital degeneracies is resolved via a quadrupole-field perturbation that nonetheless rigorously preserves energy conservation. Second, the resulting orbitals are shown to evolve adiabatically, in spite of the "preservation of character" concept that undergirds a projection of neighboring steps' MOs. The method is tested on water clusters, which exhibit considerable dynamic degeneracies, as well as a classic organic nucleophilic substitution reaction, in which the adiabatic evolution of the bonding orbitals clarifies textbook interpretations of the electronic structure during this reactive collision.

The copper hydroxide ion, CuOH+, serves as the catalytic core in several recently developed water-splitting catalysts, and an understanding of its chemistry is critical to determining viable cataly...

Chemical activation of water by a single chlorine atom was examined computationally for clusters of chlorine radicals and water in a size regime just prior to internal hydration of water/ions, Cl·(H2O)n=4-8,17. This investigation follows a recent analysis of this radical-molecule interaction [Christensen et al. J. Phys. Chem. A 2019, 123, 8657] for n = 1-4, which demonstrated that n = 4 marked a transition in which an oxidized-water structural motif became viable, albeit high in energy. Thousands of unique isomers were computed in the present analysis, which resulted in three structural classes of isomers, including intact hydrated chlorine, hydrogen-transferred (HCl)(OH·)(H2O)n-1, and charge-transferred (Cl-)(H3O+)(OH·)(H2O)n-2 configurations. The electronic structures of these classes were investigated, along with harmonic vibrational signatures that probed the degree of water-network perturbations and generated experimentally verifiable computational predictions. The main outcome of this analysis is that the charge-transferred isomers were stabilized considerably upon increased hydration-leading to an energetic crossover with the hydrogen-transferred forms-but the degree of hydration was surprisingly still not sufficient to achieve crossover between the intact chlorine-water complexes and these charge-separated configurations. Internal hydration of the ions appears to be necessary in order to achieve this separation, which will likely occur at larger cluster sizes.

The gas-phase vibrational spectrum of the isolated iodide–water cluster ion (I–·H2O), first reported in 1996, presents one of the most difficult, long-standing spectroscopic puzzles involving ion m...

This article summarizes technical advances contained in the fifth major release of the Q-Chem quantum chemistry program package, covering developments since 2015. A comprehensive library of exchange–correlation functionals, along with a suite of correlated many-body methods, continues to be a hallmark of the Q-Chem software. The many-body methods include novel variants of both coupled-cluster and configuration-interaction approaches along with methods based on the algebraic diagrammatic construction and variational reduced density-matrix methods. Methods highlighted in Q-Chem 5 include a suite of tools for modeling core-level spectroscopy, methods for describing metastable resonances, methods for computing vibronic spectra, the nuclear–electronic orbital method, and several different energy decomposition analysis techniques. High-performance capabilities including multithreaded parallelism and support for calculations on graphics processing units are described. Q-Chem boasts a community of well over 100 active academic developers, and the continuing evolution of the software is supported by an “open teamware” model and an increasingly modular design. This article summarizes technical advances contained in the fifth major release of the Q-Chem quantum chemistry program package, covering developments since 2015. A comprehensive library of exchange-correlation functionals, along with a suite of correlated many-body methods, continues to be a hallmark of the Q-Chem software. The many-body methods include novel variants of both coupled-cluster and configuration-interaction approaches along with methods based on the algebraic diagrammatic construction and variational reduced density-matrix methods. Methods highlighted in Q-Chem 5 include a suite of tools for modeling core-level spectroscopy, methods for describing metastable resonances, methods for computing vibronic spectra, the nuclear-electronic orbital method, and several different energy decomposition analysis techniques. High-performance capabilities including multithreaded parallelism and support for calculations on graphics processing units are described. Q-Chem boasts a community of well over 100 active academic developers, and the continuing evolution of the software is supported by an "open teamware" model and an increasingly modular design.

The ab initio molecular dynamics (AIMD) method provides a computational route for the real-time simulation of reactive chemistry. An often-overlooked capability of this approach is the opportunity to examine the electronic evolution of a chemical system. For AIMD trajectories based on Hartree-Fock or density functional theory methods, the real-time evolution of single-particle molecular orbitals (MOs) can provide detailed insights into the time-dependent electronic structure of molecules. The evolving electronic Hamiltonians at each MD step pose problems for tracking and visualizing a given MO's character, ordering, and associated phase throughout an MD trajectory, however. This report presents and assesses a simple algorithm for correcting these deficiencies by exploiting similarity projections of the electronic structure between neighboring MD steps. Two aspects bring this analysis beyond a simple step-to-step projection scheme. First, the challenging case of coincidental orbital degeneracies is resolved via a quadrupole-field perturbation that nonetheless rigorously preserves energy conservation. Second, the resulting orbitals are shown to evolve adiabatically, in spite of the "preservation of character" concept that undergirds a projection of neighboring steps' MOs. The method is tested on water clusters, which exhibit considerable dynamic degeneracies, as well as a classic organic nucleophilic substitution reaction, in which the adiabatic evolution of the bonding orbitals clarifies textbook interpretations of the electronic structure during this reactive collision.

The differential diagnoses for eosinophilia include allergic, infectious, autoimmune, and neoplastic diseases. We presented the case of a 79-year-old man with eosinophilia and elevated immunoglobulin E that persisted despite adequate treatment for possible environmental exposures. Further specialized testing based on his initial workup led to his diagnosis. This case highlights the importance of sequential and targeted testing to evaluate for rare causes of eosinophilia.

The partial chemical activation of water by reactive radicals was examined computationally for small clusters of chlorine and water, Cl•(H2O)n=1–4. Using an automated isomer-search procedure, dozen...

The 1,3-diaza-2,4-diborobutane (NBNB) molecule serves as the smallest model complex of an intramolecular "dihydrogen bond," which involves a nominally hydrogen-bonding interaction between amine and borane hydrogen atoms. In the present study, the role of this dihydrogen bond in influencing the inherent molecular dynamics of NBNB is investigated computationally with ab initio molecular dynamics and path integral molecular dynamics techniques, as well as vibrational spectra analysis and static quantum chemistry computations. These simulations indicate that the dihydrogen-bonding interaction impacts both the high- and low-frequency motions of the molecule, with the dominant motions involving low-frequency backbone isomerization and terminal amine rotation. Geometric isotope effects were found to be modest. The analysis also addresses the paradoxical fostering of amine rotation via a relatively strong dihydrogen bond interaction. Electrostatic and geometric factors most directly explain this effect, and although some orbital evidence was found for a small covalent component of this interaction, the dynamics and electronic structure suggest that electrostatic contributions are the controlling factors for molecular motion in NBNB.

The copper hydroxide ion, CuOH

A quantitative description of the interactions between ions and water is key to characterizing the role played by ions in mediating fundamental processes that take place in aqueous environments. At the molecular level, vibrational spectroscopy provides a unique means to probe the multidimensional potential energy surface of small ion-water clusters. In this study, we combine the MB-nrg potential energy functions recently developed for ion-water interactions with perturbative corrections to vibrational self-consistent field theory and the local-monomer approximation to disentangle many-body effects on the stability and vibrational structure of the Cs

Chemical activation of water by a single chlorine atom was examined computationally for clusters of chlorine radicals and water in a size regime just prior to internal hydration of water/ions, Cl

PURPOSE: Although Common Variable Immunodeficiency (CVID) is considered the most prevalent symptomatic primary antibody deficiency (PAD), there is a population with symptomatic PADs that do not meet criteria for CVID. We analyzed clinical and immunological profiles of patients with different PADs to better understand the differences and similarities between CVID and other PADs. METHODS: We extracted clinical and laboratory data of patients with PADs from electronic medical records. Patients were categorized into CVID, IgG subclass 2 deficiency (IgG2D), IgG deficiency (IgGD) and selective antibody deficiency (sAbD) based on basal immunoglobulin levels and pneumococcal vaccine responses. We compared clinical and immunological characteristics in these groups. RESULTS: All patients, regardless of PAD types, showed similar frequencies of infections, bronchiectasis, and interstitial lung disease (ILD). Hematopoietic malignancies were more frequently found in the CVID than in the IgG2D, IgGD and sAbD groups, while the latter groups trended towards an increased frequency of connective tissue diseases (CTD). Low counts of natural killer (NK) cells were associated with malignancy, autoimmunity, and ILD in CVID but not in other PAD groups. CONCLUSIONS: Higher frequency of hematopoietic malignancy in CVID than in the other PADs and association of lower NK cell counts with non-infectious complications in CVID suggest a relationship between immune alterations and the development of non-infectious manifestations in PADs.

Characterizing structural and phase transformations of water at the molecular level is key to understanding a variety of multiphase processes ranging from ice nucleation in the atmosphere to hydration of biomolecules and wetting of solid surfaces. In this study, state-of-the-art quantum simulations with a many-body water potential energy surface, which exhibits chemical and spectroscopic accuracy, are carried out to monitor the microscopic melting of the water hexamer through the analysis of vibrational spectra and appropriate structural order parameters as a function of temperature. The water hexamer is specifically chosen as a case study due to the central role of this cluster in the molecular-level understanding of hydrogen bonding in water. Besides being in agreement with the experimental data available for selected isomers at very low temperature, the present results provide quantitative insights into the interplay between energetic, entropic, and nuclear quantum effects on the evolution of water clusters from "solid-like" to "liquid-like" structures. This study thus demonstrates that computer simulations can now bridge the gap between measurements currently possible for individual isomers at very low temperature and observations of isomer mixtures at ambient conditions.

The partial chemical activation of water by reactive radicals was examined computationally for small clusters of chlorine and water, Cl

The isomers of a hydrated Cu(I) ion with n = 1–10 water molecules were investigated by using ab initio quantum chemistry and an automated isomer-search algorithm. The electronic structure and vibrational spectra of the hundreds of resulting isomers were used to analyze the source of the observed bonding patterns. A structural evolution from dominantly two-coordinate structures (n = 1–4) toward a mixture of two- and three-coordinate structures was observed at n = 5–6, where the stability provided by expanded hydrogen-bonding was competitive with the dominantly electrostatic interaction between the water ligand and remaining binding sites of the metal ion. Further hydration (n = 7–10) led to a mixture of three- and four-coordinate structures. The metal ion was found, through spectroscopic signatures, to appreciably perturb the O–H bonds of even third-shell water molecules, which highlighted the ability of this nominally simple ion to partially activate the surrounding water network.

Acceleration of ab initio molecular dynamics (AIMD) simulations can be reliably achieved by extrapolation of electronic data from previous timesteps. Existing techniques utilize polynomial least-squares regression to fit previous steps’ Fock or density matrix elements. In this work, the recursive Burg ‘linear prediction’ technique is shown to be a viable alternative to polynomial regression, and the extrapolation-predicted Fock matrix elements were three orders of magnitude closer to converged elements. Accelerations of 1.8–3.4× were observed in test systems, and in all cases, linear prediction outperformed polynomial extrapolation. Importantly, these accelerations were achieved without reducing the MD integration timestep.

The structures, properties, and spectroscopic signatures of oxidized water clusters,(H2O)+n=6–21, are examined in this work, to provide fundamental insight into renewable energy and radiological processes. Computational quantum chemistry approaches are employed to sample cluster morphologies, yielding hundreds of low-lying isomers with low barriers to interconversion. The ion–radical pair-separation trend, however, which was observed in previous computational studies and in small-cluster spectroscopy experiments, is shown to continue in this larger cluster size regime. The source of this trend is preferential solvation of the hydronium ion by water, including effects beyond the first solvation shell. The fundamental conclusion of this work, therefore, is that the initially formed ion–radical dimer, which has served as a prototypical model of oxidized water, is a nascent species in large, oxidized water clusters and, very likely, bulk water.

The cation dimer of water and hydrogen sulfide, [(H2O)(H2S)]+, serves as a fundamental model for the oxidation chemistry of H2S. The known oxidative metabolism of H2S by biological species in sulfur-rich environments has motivated the study of the inherent properties of this benchmark complex, with possible mechanistic implications for modern water oxidation chemistry. The low-energy isomer of this open-shell ion is a proton-transferred (PT) structure, H3O+⋯SH˙. An alternative PT structure, H3S+⋯OH˙, and a hemibonded (HB) isomer, [H2O·SH2]+, are also stable isomers, placing this complex intermediate to known (H2O)2+ (PT) and (H2S)2+ (HB) limiting regimes. This intermediate character suggested the possibility of unique molecular motion, even in the vibrational ground state. Path integral molecular dynamics and anharmonic vibrational spectroscopy simulations have been performed in this study, in order to understand the inherent quantum molecular motion of this complex. The resulting structural distributions were found to deviate significantly from both classical and harmonic analyses, including the observation of large-amplitude anharmonic motion of the central proton and nearly free rotation of the terminal hydrogens. The predicted vibrational spectra are particularly unique and suggest characteristic signatures of the strong electronic interactions and anharmonic vibrational mode couplings in this radical cation.

This work describes an approach to accelerate ab initio Born-Oppenheimer molecular dynamics (MD) simulations by exploiting the inherent timescale separation between contributions from different atom-centered Gaussian basis sets. Several MD steps are propagated with a cost-efficient, low-level basis set, after which a dynamical correction accounts for large basis set relaxation effects in a time-reversible fashion. This multiple-timestep scheme is shown to generate valid MD trajectories, on the basis of rigorous testing for water clusters, the methanol dimer, an alanine polypeptide, protonated hydrazine, and the oxidized water dimer. This new approach generates observables that are consistent with those of target basis set trajectories, including MD-based vibrational spectra. This protocol is shown to be valid for Hartree-Fock, density functional theory, and second-order Møller-Plesset perturbation theory approaches. Recommended pairings include 6-31G as a low-level basis set for 6-31G** or 6-311G**, as well as cc-pVDZ as the subset for accurate dynamics with aug-cc-pVTZ. Demonstrated cost savings include factors of 2.6-7.3 on the systems tested and are expected to remain valid across system sizes.

Ionized water clusters serve as a model of water-splitting chemistry for energetic purposes, as well as postradiolytic events in condensed-phase systems. Structures, properties, and relative energies are presented for oxidized water clusters, (H2O)n=1-5(+), using equation-of-motion coupled-cluster theory approaches. In small clusters, an ion-radical contact pair OH···H3O+ is known to form upon ionization. The transition from n = 4 to n = 5 molecules in the cluster, however, is found to demarcate a size regime in which a propensity for the ion and radical to separate exists. This trend is consistent with recent experimental vibrational analyses. Decomposition of the cluster energetics reveals that preferential solvation of the hydronium cation by water serves as the dominant driving force for this pair separation, which should persist in larger clusters and bulk water ionization.

The dynamic, quantum structure of [Mg(H2)n=1–6]2+complexes is investigated via ab initio path integral molecular dynamics simulations. These complexes represent the strong, σ-complex regime of meta...

In combined quantum mechanical/molecular mechanical (QM/MM) free energy calculations, it is often advantageous to have a frozen geometry for the quantum mechanical (QM) region. For such multiple-environment single-system (MESS) cases, two schemes are proposed here for estimating the polarization energy: the first scheme, termed MESS-E, involves a Roothaan step extrapolation of the self-consistent field (SCF) energy; whereas the other scheme, termed MESS-H, employs a Newton-Raphson correction using an approximate inverse electronic Hessian of the QM region (which is constructed only once). Both schemes are extremely efficient, because the expensive Fock updates and SCF iterations in standard QM/MM calculations are completely avoided at each configuration. They produce reasonably accurate QM/MM polarization energies: MESS-E can predict the polarization energy within 0.25 kcal/mol in terms of the mean signed error for two of our test cases, solvated methanol and solvated β-alanine, using the M06-2X or ωB97X-D functionals; MESS-H can reproduce the polarization energy within 0.2 kcal/mol for these two cases and for the oxyluciferin-luciferase complex, if the approximate inverse electronic Hessians are constructed with sufficient accuracy.

The water dimer cation, (H2O)2+, has long served as a prototypical reference system for water oxidation chemistry. In spite of this status, a definitive explanation for the anomalous—and dominant—features in the experimental vibrational spectrum [Gardenier, G. H.; Johnson, M. A.; McCoy, A. B. J. Phys. Chem. A, 2009, 113, 4772–4779] has not been determined, and harmonic analyses qualitatively fail to reproduce these features. In this computational study, accurate quantum chemistry methods are combined with a fully coupled, six-dimensional anharmonic model to show that the unassigned bands are the result of resonant mode interactions and strong anharmonic coupling. Such coupling is fundamentally due to the unique electronic structure of this open-shell ion and the manner in which auxiliary modes affect the natural charge-transfer properties of the shared-proton stretch. These unique vibrational signatures provide a key reference point for modern spectroscopic and mechanistic analyses of water-oxidation cata...

Because of both experimental and computational challenges, protonated tryptophan has remained the last aromatic amino acid for which the intrinsic structures of low-energy conformers have not been unambiguously solved. The IR-IR-UV hole-burning spectroscopy technique has been applied to overcome the limitations of the commonly used IR-UV double resonance technique and to measure conformer-specific vibrational spectra of TrpH(+), cooled to T = 10 K. Anharmonic ab initio vibrational spectroscopy simulations unambiguously assign the dominant conformers to the two lowest-energy geometries from benchmark coupled-cluster structure computations. The match between experimental and ab initio spectra provides an unbiased validation of the calculated structures of the two experimentally observed conformers of this benchmark ion. Furthermore, the vibrational spectra provide conformer-specific signatures of the stabilizing interactions, including hydrogen bonding and an intramolecular cation-π interaction.

This work investigates the use of multiple-timestep schemes in imaginary time for computationally efficient ab initio equilibrium path integral simulations of quantum molecular motion. In the simplest formulation, only every n(th) path integral replica is computed at the target level of electronic structure theory, whereas the remaining low-level replicas still account for nuclear motion quantum effects with a more computationally economical theory. Motivated by recent developments for multiple-timestep techniques in real-time classical molecular dynamics, both 1-electron (atomic-orbital basis set) and 2-electron (electron correlation) truncations are shown to be effective. Structural distributions and thermodynamic averages are tested for representative analytic potentials and ab initio molecular examples. Target quantum chemistry methods include density functional theory and second-order Møller-Plesset perturbation theory, although any level of theory is formally amenable to this framework. For a standard two-level splitting, computational speedups of 1.6-4.0x are observed when using a 4-fold reduction in time slices; an 8-fold reduction is feasible in some cases. Multitiered options further reduce computational requirements and suggest that quantum mechanical motion could potentially be obtained at a cost not significantly different from the cost of classical simulations.

Polynomial extrapolation of response (‘z-vector’) elements is shown to reduce the cost of correlated-wavefunction, classical ab initio molecular dynamics. Demonstrations with resolution-of-the-identity Moller–Plesset perturbation theory (RI-MP2) show that the number of response equation iterations is reduced by a factor of 2–3, thereby enabling accelerated MP2 dynamics. Coupled with previously demonstrated Fock matrix extrapolation, the combined iterative SCF and z-vector calculations are reduced to a minority share of the total calculation. Though demonstrated for MP2, these methods can also be generalized to higher levels of electron correlation or excited state methods.

It's the Network Numerous reactions of small molecules and ions in the atmosphere take place in the confines of watery aerosols. Relph et al. (p. 308 ; see the Perspective by Siefermann and Abel ) explored the specific influence of a water cluster's geometry on the transformation of solvated nitrosonium (NO + ) to nitrous acid (HONO). The reaction involves (O)N–O(H) bond formation with one water molecule, concomitant with proton transfer to additional, surrounding water molecules. Vibrational spectroscopy and theoretical simulations suggest that certain arrangements of the surrounding water network are much more effective than others in accommodating this charge transfer, and thus facilitating the reaction.

Ground state structures with side-on nitrosyl ({eta}{sup 2}-NO) and isonitrosyl (ON) ligands have been observed in a variety of transition-metal complexes. In contrast, excited state structures with bent-NO ligands have been proposed for years but never directly observed. Here we use picosecond time-resolved infrared spectroscopy and density functional theory (DFT) modeling to study the photochemistry of Co(CO){sub 3}(NO), a model transition-metal-NO compound. Surprisingly, we have observed no evidence for ON and {eta}{sup 2}-NO structural isomers, but have observed two bent-NO complexes. DFT modeling of the ground and excited state potentials indicates that the bent-NO complexes correspond to triplet excited states. Photolysis of Co(CO){sub 3}(NO) with a 400-nm pump pulse leads to population of a manifold of excited states which decay to form an excited state triplet bent-NO complex within 1 ps. This structure relaxes to the ground triplet state in ca. 350 ps to form a second bent-NO structure.

The feasibility of the strongest possible dual-basis approximation to polarized valence double zeta Hartree–Fock and density functional theory calculations is explored. Specifically, to approximate...

In this work, we present the analytical gradient of dual-basis second-order Moller–Plesset perturbation theory within the resolution-of-the-identity approximation (DB-RI-MP2). Interestingly, analytical DB-RI-MP2 gradient theory involves significant changes to both the theory and computation of the coupled-perturbed self-consistent field equations (CPSCF). From a theoretical point of view, the number of orbital responses required in DB-RI-MP2 analytical gradient theory has been reduced to the product of the number of occupied and virtual orbitals determined by the rank of the small atomic orbital (AO) basis. From a computational point of view, the DB-CPSCF equations can be solved within this smaller space at a fraction of the computational cost. Additional computational savings can be obtained during the digestion of the four-centered AO integral derivatives and the efficient underlying DB-SCF procedure, which lead to a significant overall reduction in the computational cost necessary for treating molecula...

We present a new algorithm for analytical gradient evaluation in resolution-of-the-identity second-order Moller-Plesset perturbation theory (RI-MP2) and thoroughly assess its computational performance and chemical accuracy. This algorithm addresses the potential I/O bottlenecks associated with disk-based storage and access of the RI-MP2 t-amplitudes by utilizing a semi-direct batching approach and yields computational speed-ups of approximately 2-3 over the best conventional MP2 analytical gradient algorithms. In addition, we attempt to provide a straightforward guide to performing reliable and cost-efficient geometry optimizations at the RI-MP2 level of theory. By computing relative atomization energies for the G3/99 set and optimizing a test set of 136 equilibrium molecular structures, we demonstrate that satisfactory relative accuracy and significant computational savings can be obtained using Pople-style atomic orbital basis sets with the existing auxiliary basis expansions for RI-MP2 computations. We also show that RI-MP2 geometry optimizations reproduce molecular equilibrium structures with no significant deviations (>0.1 pm) from the predictions of conventional MP2 theory. As a chemical application, we computed the extended-globular conformational energy gap in alanine tetrapeptide at the extrapolated RI-MP2/cc-pV(TQ)Z level as 2.884, 4.414, and 4.994 kcal/mol for structures optimized using the HF, DFT (B3LYP), and RI-MP2 methodologies and the cc-pVTZ basis set, respectively. These marked energetic discrepancies originate from differential intramolecular hydrogen bonding present in the globular conformation optimized at these levels of theory and clearly demonstrate the importance of long-range correlation effects in polypeptide conformational analysis.

We report the geometries of two distorted T-shaped benzene dimer structures optimized at the RI-MP2/aug-cc-pVTZ level of theory. At the extrapolated RI-MP2/aug-cc-pV(TQ)Z level, the Cs over atom and Cs over bond configurations were found to be lower in energy than the conventionally accepted C2v T-shaped structure by 0.146 and 0.163 kcal/mol, respectively. When DCCSD(T)/6-311+G(2df,p) corrections were included, these structures remained lower in energy than the C2v reference by 0.127 and 0.132 kcal/mol, respectively, with Cs over bond as the minimum energy T-shaped structure. While not the focus of this Letter, we also report that the C2v T-shaped configuration is stabilized by 0.31 kcal/mol over the C2h parallel-displaced configuration at the DCCSD(T)/aug-cc-pVTZ approximation to the CCSD(T)/CBS limit. � 2007 Elsevier B.V. All rights reserved.

We present the local charge state modification at room temperature of small insulator-supported molecular ensembles formed by 1,1'-ferrocenedicarboxylic acid on calcite. Single electron tunnelling between the conducting tip of a noncontact atomic force microscope (NC-AFM) and the molecular islands is observed. By joining NC-AFM with Kelvin probe force microscopy, successive charge build-up in the sample is observed from consecutive experiments. Charge transfer within the islands and structural relaxation of the adsorbate/surface system is suggested by the experimental data.

Basis set pairings for dual-basis calculations are presented for the aug-cc-pVXZ (X = D, T, Q) series of basis sets. Fidelity with single-basis results is assessed at the second-order Møller-Plesset perturbation theory (MP2) level within the resolution-of-the-identity (RI) approximation, using the S22 set of noncovalent interactions and a series of electron affinities from the G3 set. Root-mean-squared errors for the S22 set are 0.019 kcal mol(-1) or lower, with a maximum deviation of 0.44%, and errors in nuclear structures are 0.09% or lower. Cost savings of 60-93% (RI-MP2 energies) and 50-88% (RI-MP2 gradients) are demonstrated. Spin-component-scaled MP2 [SCS(MI)-MP2] scaling parameters are provided for the aug-cc-pVXZ series, and dual-basis results are shown to be consistent without reoptimization of the single-basis parameters. Explicit handling of linear dependence in the basis set projection scheme is also provided. These dual-basis pairings will be helpful for accelerating accurate Hartree-Fock, density functional theory (DFT), MP2 and scaled MP2, and so-called doubly hybrid DFT calculations of intermolecular interactions (and other systems), where augmented basis sets are physically important.

A multiple-timestep ab initio molecular dynamics scheme based on varying the two-electron integral screening method used in Hartree–Fock or density functional theory calculations is presented. Although screening is motivated by numerical considerations, it is also related to separations in the length- and timescales characterizing forces in a molecular system: Loose thresholds are sufficient to describe fast motions over short distances, while tight thresholds may be employed for larger length scales and longer times, leading to a practical acceleration of ab initio molecular dynamics simulations. Standard screening approaches can lead, however, to significant discontinuities in (and inconsistencies between) the energy and gradient when the screening threshold is loose, making them inappropriate for use in dynamics. To remedy this problem, a consistent window-screening method that smooths these discontinuities is devised. Further algorithmic improvements reuse electronic-structure information within the dynamics step and enhance efficiency relative to a naı̈ve multiple-timestepping protocol. The resulting scheme is shown to realize meaningful reductions in the cost of Hartree–Fock and B3LYP simulations of a moderately large system, the protonated sarcosine/glycine dipeptide embedded in a 19-water cluster. This document is the unedited Author's version of a Submitted Work that was subsequently accepted for publication in Journal of Chemical Theory and Computation, copyright © American Chemical Society after peer review. To access the final edited and published work see http://pubs.acs.org/articlesonrequest/AOR-3PynRTiASCcZCZep2V3h.

International audience; A summary of the technical advances that are incorporated in the fourth major release of the Q-Chem quantum chemistry program is provided, covering approximately the last seven years. These include developments in density functional theory methods and algorithms, nuclear magnetic resonance (NMR) property evaluation, coupled cluster and perturbation theories, methods for electronically excited and open-shell species, tools for treating extended environments, algorithms for walking on potential surfaces, analysis tools, energy and electron transfer modelling, parallel computing capabilities, and graphical user interfaces. In addition, a selection of example case studies that illustrate these capabilities is given. These include extensive benchmarks of the comparative accuracy of modern density functionals for bonded and non-bonded interactions, tests of attenuated second order Moller-Plesset (MP2) methods for intermolecular interactions, a variety of parallel performance benchmarks, and tests of the accuracy of implicit solvation models. Some specific chemical examples include calculations on the strongly correlated Cr-2 dimer, exploring zeolite-catalysed ethane dehydrogenation, energy decomposition analysis of a charged ter-molecular complex arising from glycerol photoionisation, and natural transition orbitals for a Frenkel exciton state in a nine-unit model of a self-assembling nanotube.

Analytic gradients of dual-basis Hartree-Fock and density functional theory energies have been derived and implemented, which provide the opportunity for capturing large basis-set gradient effects at reduced cost. Suggested pairings for gradient calculations are 6-31G/6-31G**, dual[-f,-d]/cc-pVTZ, and 6-311G*/6-311 + +G(3df,3pd). Equilibrium geometries are produced within 0.0005 A of large-basis results for the latter two pairings. Though a single, iterative SCF response equation must be solved (unlike standard SCF gradients), it may be obtained in the smaller basis set, and integral screening further reduces the cost for well-chosen subsets. Total nuclear force calculations exhibit up to 75% savings, relative to large-basis calculations.

Local-mode coordinates have previously been shown to be an effective starting point for anharmonic vibrational spectroscopy calculations. This general approach borrows techniques from localized-orbital machinery in electronic structure theory and generates a new set of spatially localized vibrational modes. These modes exhibit a well-behaved spatial decay of anharmonic mode couplings, which, in turn, allows for a systematic, a priori truncation of couplings and increased computational efficiency. Fully localized modes, however, have been found to lead to unintuitive mixtures of characteristic motions, such as stretches and bends, and accordingly large bilinear couplings. In this work, a very simple, tunable localization frequency window is introduced, in order to realize the transition from normal modes to fully localized modes. Partial localization can be achieved by localizing only pairs of modes within this traveling frequency window, which allows for intuitive interpretation of modes. The optimal window size is suggested to be a few hundreds of wave numbers, based on small- to medium-sized test systems, including water clusters and polypeptides. The new sets of partially localized coordinates retain their spatial coupling decay behavior while providing a reduced number of potential energy evaluations for convergence of anharmonic spectra.

A “tiered” approach to Monte Carlo sampling of nuclear configurations is presented for ab initio, self-consistent field (SCF)-based potentials, including Hartree-Fock and density functional theory. Rather than Metropolis testing only the final SCF energy, individual cycle energies are tested in a tiered fashion, without approximation. Accordingly, rejected configurations are terminated early in the SCF procedure. The method is shown to properly obey detailed balance, and effective modifications are presented for cases in which the initial SCF guess is particularly poor. Demonstrations on simple systems are provided, including an assessment of the thermal properties of the neutral water dimer with B3LYP/6-31++G**. Cost analysis indicates a factor-of-two reduction in SCF cycles, which makes the method competitive with accelerated molecular dynamics sampling techniques, without the need for forces.