Czech Academy of Sciences, J. Heyrovský Institute of Physical Chemistry

ADVERTISEMENT RETURN TO ISSUEPREVArticleBlue-Shifting Hydrogen BondsPavel Hobza and Zdeněk HavlasView Author Information J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, 182 23 Prague 8, Czech Republic, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 166 10 Prague 6, Czech Republic, and Center for Complex Molecular Systems and Biomolecules, 182 23 Prague 8, Czech Republic Cite this: Chem. Rev. 2000, 100, 11, 4253–4264Publication Date (Web):September 14, 2000Publication History Received14 January 2000Published online14 September 2000Published inissue 1 November 2000https://pubs.acs.org/doi/10.1021/cr990050qhttps://doi.org/10.1021/cr990050qresearch-articleACS PublicationsCopyright © 2000 American Chemical SocietyRequest reuse permissionsArticle Views9399Altmetric-Citations1611LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose SUBJECTS:Aromatic compounds,Chemical structure,Electron density,Hydrocarbons,Hydrogen Get e-Alerts

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTNoncovalent Interactions: A Challenge for Experiment and TheoryKlaus Müller-Dethlefs and Pavel HobzaView Author Information Department of Chemistry, University of York, Heslington, York YO10 5DD, United Kingdom, and J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, 182 23 Praha, Czech Republic Cite this: Chem. Rev. 2000, 100, 1, 143–168Publication Date (Web):December 18, 1999Publication History Received8 September 1999Revised11 November 1999Published online18 December 1999Published inissue 1 January 2000https://pubs.acs.org/doi/10.1021/cr9900331https://doi.org/10.1021/cr9900331research-articleACS PublicationsCopyright © 2000 American Chemical SocietyRequest reuse permissionsArticle Views11259Altmetric-Citations1526LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose SUBJECTS:Chemical structure,Cluster chemistry,Energy,Molecular structure,Noncovalent interactions Get e-Alerts

Practical challenges in simulating quantum systems on classical computers have been widely recognized in the quantum physics and quantum chemistry communities over the past century. Although many approximation methods have been introduced, the complexity of quantum mechanics remains hard to appease. The advent of quantum computation brings new pathways to navigate this challenging and complex landscape. By manipulating quantum states of matter and taking advantage of their unique features such as superposition and entanglement, quantum computers promise to efficiently deliver accurate results for many important problems in quantum chemistry, such as the electronic structure of molecules. In the past two decades, significant advances have been made in developing algorithms and physical hardware for quantum computing, heralding a revolution in simulation of quantum systems. This Review provides an overview of the algorithms and results that are relevant for quantum chemistry. The intended audience is both quantum chemists who seek to learn more about quantum computing and quantum computing researchers who would like to explore applications in quantum chemistry.

Practical challenges in simulating quantum systems on classical computers have been widely recognized in the quantum physics and quantum chemistry communities over the past century. Although many approximation methods have been introduced, the complexity of quantum mechanics remains hard to appease. The advent of quantum computation brings new pathways to navigate this challenging complexity landscape. By manipulating quantum states of matter and taking advantage of their unique features such as superposition and entanglement, quantum computers promise to efficiently deliver accurate results for many important problems in quantum chemistry such as the electronic structure of molecules. In the past two decades significant advances have been made in developing algorithms and physical hardware for quantum computing, heralding a revolution in simulation of quantum systems. This article is an overview of the algorithms and results that are relevant for quantum chemistry. The intended audience is both quantum chemists who seek to learn more about quantum computing, and quantum computing researchers who would like to explore applications in quantum chemistry.

We extend an approximate density functional theory (DFT) method for the description of long-range dispersive interactions which are normally neglected by construction, irrespective of the correlation function applied. An empirical formula, consisting of an R−6 term is introduced, which is appropriately damped for short distances; the corresponding C6 coefficient, which is calculated from experimental atomic polarizabilities, can be consistently added to the total energy expression of the method. We apply this approximate DFT plus dispersion energy method to describe the hydrogen bonding and stacking interactions of nucleic acid base pairs. Comparison to MP2/6-31G*(0.25) results shows that the method is capable of reproducing hydrogen bonding as well as the vertical and twist dependence of the interaction energy very accurately.

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTStructure, Energetics, and Dynamics of the Nucleic Acid Base Pairs: Nonempirical Ab Initio CalculationsPavel Hobza and Jiří ŠponerView Author Information J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, 182 23 Prague 8, Czech Republic Cite this: Chem. Rev. 1999, 99, 11, 3247–3276Publication Date (Web):October 13, 1999Publication History Received2 March 1999Revised29 June 1999Published online13 October 1999Published inissue 10 November 1999https://pubs.acs.org/doi/10.1021/cr9800255https://doi.org/10.1021/cr9800255research-articleACS PublicationsCopyright © 1999 American Chemical SocietyRequest reuse permissionsArticle Views3988Altmetric-Citations932LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose SUBJECTS:Basis sets,Energy,Interaction energies,Oligomers,Stabilization Get e-Alerts

Selected ion flow tube mass spectrometry (SIFT-MS) is a new analytical technique for the real-time quantification of several trace gases simultaneously in air and breath. It relies on chemical ionization of the trace gas molecules in air/breath samples introduced into helium carrier gas using H(3)O(+), NO(+), and O(2) (+.) precursor ions. Reactions between the precursor ions and trace gas molecules proceed for an accurately defined time, the precursor and product ions being detected and counted by a downstream mass spectrometer, thus effecting quantification. Absolute concentrations of trace gases in single breath exhalation can be determined by SIFT-MS down to ppb levels, obviating sample collection and calibration. Illustrative examples of SIFT-MS studies include (i) analysis of gases from combustion engines, animals and their waste, and food; (ii) breath and urinary headspace studies of metabolites, ethanol metabolism, elevated acetone during ovulation, and exogenous compounds; and (iii) urinary infection and the presence of tumors, the influence of dialysis on breath ammonia, acetone, and isoprene, and acetaldehyde released by cancer cells in vitro. Flowing afterglow mass spectrometry (FA-MS) is briefly described, which allows on-line quantification of deuterium in breath water vapor.

We present results from theoretical studies of aqueous ionic solvation of alkali halides aimed at developing a microscopic description of structure and dynamics at the interface between air and salt solutions. The traditional view has depicted the air/solution interface of simple electrolytes as being devoid of ions. However, it is now firmly established that polarizable anions, such as the heavier halides, occupy the surface of small to medium sized water clusters. Using a combination of theoretical calculations, including ab initio quantum chemistry, Car−Parrinello molecular dynamics simulations, and primarily molecular dynamics simulations based on polarizable force fields, we present a unified view of the interfacial structure of aqueous ionic clusters and bulk solutions. Indeed, we demonstrate that the heavier halogen anions have a propensity for the interface that is proportional to their polarizability. The cluster results are directly supported by existing experimental and theoretical studies, and the bulk solution results are indirectly supported by several recent experiments. The novel view of the ionic solution/air interface presented here has also implications for dynamics following photoexcitation and electron photodetachment of ions. Moreover, the present results provide insight into heterogeneous atmospheric chemistry leading to halogen release from sea salt aerosols in the lower marine troposphere and from the Arctic snowpack during polar sunrise.

Zeolites are well-known as valuable crystalline solids with framework structures containing discrete micropores of molecular dimensions that accommodate exchangeable extraframework cation sites.1−3 In terms of host−guest interactions, zeolites can be viewed as host frameworks with structurally intact and immutable three-dimensional (3D) structures. They show exceptional catalytic and sorption characteristics together with very desirable environmental qualities.4−7 Zeolites are widely used in commercial applications as catalysts for hydrocarbon conversions in petroleum and chemical industries, 8−10 as sorbents for small-molecule separation processes, and as ion exchangers in detergents.11

A combination of experimental, molecular dynamics, and kinetics modeling studies is applied to a system of concentrated aqueous sodium chloride particles suspended in air at room temperature with ozone, irradiated at 254 nanometers to generate hydroxyl radicals. Measurements of the observed gaseous molecular chlorine product are explainable only if reactions at the air-water interface are dominant. Molecular dynamics simulations show the availability of substantial amounts of chloride ions for reaction at the interface, and quantum chemical calculations predict that in the gas phase chloride ions will strongly attract hydroxl radicals. Model extrapolation to the marine boundary layer yields daytime chlorine atom concentrations that are in good agreement with estimates based on field measurements of the decay of selected organics over the Southern Ocean and the North Atlantic. Thus, ion-enhanced interactions with gases at aqueous interfaces may play a more generalized and important role in the chemistry of concentrated inorganic salt solutions than was previously recognized.

Most salts raise the surface tension of water. Interpretation of this phenomenon via the Gibbs adsorption equation has led to the commonly held belief that the ions are repelled from the air/solution interface. Here, we report results from molecular dynamics simulations of a series of sodium halide solution/air interfaces. The simulations reproduce the experimentally measured increases in surface tension relative to pure water. Analysis of the structure reveals that the small, nonpolarizable fluoride anion is excluded from the interface, in accord with the traditional picture. However, all of the larger, polarizable halide anions are present at the interface, and bromide and iodide actually have higher concentrations in the interfacial region than in the bulk. On the basis of the simulations we develop a molecular picture of hydrogen bonding in the interfacial region that might be tested by surface sensitive spectroscopic experiments. The novel, microscopic view of the interfacial structure of aqueous salt solutions presented in this paper has implications for the reactivity of sea salt aerosols in the marine boundary layer, and bromine chemistry in the remote Arctic at polar sunrise.

Specialized computational chemistry packages have permanently reshaped the landscape of chemical and materials science by providing tools to support and guide experimental efforts and for the prediction of atomistic and electronic properties. In this regard, electronic structure packages have played a special role by using first-principle-driven methodologies to model complex chemical and materials processes. Over the past few decades, the rapid development of computing technologies and the tremendous increase in computational power have offered a unique chance to study complex transformations using sophisticated and predictive many-body techniques that describe correlated behavior of electrons in molecular and condensed phase systems at different levels of theory. In enabling these simulations, novel parallel algorithms have been able to take advantage of computational resources to address the polynomial scaling of electronic structure methods. In this paper, we briefly review the NWChem computational chemistry suite, including its history, design principles, parallel tools, current capabilities, outreach, and outlook.

It is proposed that the benzene dimer has two almost isoenergetic structures. This has been confirmed by very high level ab initio calculations. MP2, MP4, and CCSD(T) calculations with various basis sets up to the augmented correlation consistent polarized double-zeta (aug-cc-pvdz) one were performed for the sandwich (S), T-shaped (T), and parallel-displaced (PD) structures of the benzene dimer. MP2 strongly overestimates the stabilization energy and leads to incorrect global minimum. Also, the MP4 predictions differ from the CCSD(T) ones. At the CCSD(T) level the T structure was the most stable structure with stabilization energy of about 2.3 kcal/mol. The PD structure at the same level was found to be slightly less stable (by 0.2−0.3 kcal/mol). The energy difference between these structures is sensitive to the theoretical level applied, and we estimated that both structures are similarly stable. The absolute value of stabilization energy is believed to be close to the genuine value; this conclusion was based on study of basis set saturation where basis sets up to [4s3p2d1f] were utilized. Performance of existing empirical potentials is evaluated. The existence of the C−H···π H-bond was not confirmed. Finally, consequences of the existence of two similarly stable structures of the benzene dimer for the structure and function of proteins are discussed.

Six representative isotope-labeled samples of titanium dioxide were synthesized: Ti(16)O(2), Ti(17)O(2) and Ti(18)O(2), each in anatase and rutile forms. Their Raman scattering was analyzed at temperatures down to 5 K. Spectral assignment was supported by numerical simulation using DFT calculations. The combination of experimental and theoretical Raman frequencies with the corresponding isotopic shifts allowed us to address various still-open questions about the second-order Raman scattering in rutile, and the analysis of overlapping features in the anatase spectrum.

Abstract Single-atom catalysts with full utilization of metal centers can bridge the gap between molecular and solid-state catalysis. Metal-nitrogen-carbon materials prepared via pyrolysis are promising single-atom catalysts but often also comprise metallic particles. Here, we pyrolytically synthesize a Co–N–C material only comprising atomically dispersed cobalt ions and identify with X-ray absorption spectroscopy, magnetic susceptibility measurements and density functional theory the structure and electronic state of three porphyrinic moieties, CoN 4 C 12 , CoN 3 C 10,porp and CoN 2 C 5 . The O 2 electro-reduction and operando X-ray absorption response are measured in acidic medium on Co–N–C and compared to those of a Fe–N–C catalyst prepared similarly. We show that cobalt moieties are unmodified from 0.0 to 1.0 V versus a reversible hydrogen electrode, while Fe-based moieties experience structural and electronic-state changes. On the basis of density functional theory analysis and established relationships between redox potential and O 2 -adsorption strength, we conclude that cobalt-based moieties bind O 2 too weakly for efficient O 2 reduction.

Abstract Density functional theory (DFT) methods, including nonlocal density gradient terms in the exchange and correlation energy functionals, were applied to various types of molecular clusters: H‐bonded, ionic, electrostatic, and London. Reliable results on the structure and stabilization energy were obtained for the first two types of cluster as long as Becke3LYP and Becke3P86 functionals and basis sets of at least DZ + P quality were used. DFT methods with currently available functionals failed completely, however, for London‐type clusters, for which no minimum was found on the potential energy surfaces. DFT interaction energy exhibits the same basis set extension dependence as the Hartree‐Fock (HF) interaction energy. Therefore, the Boys‐Bernardi function counterpoise procedure should be employed for elimination of the DFT basis set superposition error. © 1995 John Wiley & Sons, Inc.

The Pluronic P123 templated mesoporous TiO2 film was grown via layer-by-layer deposition and characterized by a novel methodology based on the adsorption of n-pentane. Multiple-layer depositions did not perturb the mesoporous structure significantly. Our TiO2 film was sensitized by a newly developed Ru-bipyridine dye (N945) and was applied as a photoanode in dye-sensitized solar cell. The 1-microm-thick mesoporous film, made by the superposition of three layers, showed enhanced solar conversion efficiency by about 50% compared to that of traditional films of the same thickness made from randomly oriented anatase nanocrystals.

Commercial graphene nanoplatelets in the form of optically transparent thin films on F-doped SnO(2) (FTO) exhibited high electrocatalytic activity toward I(3)(-)/I(-) redox couple, particularly in electrolyte based on ionic liquid (Z952). The charge-transfer resistance, R(CT), was smaller by a factor of 5-6 in ionic liquid, compared to values in traditional electrolyte based on methoxypropionitrile solution (Z946). Optical spectra and electrochemical impedance confirm that the film's absorbance scales linearly with R(CT)(-1). Electrocatalytic properties of graphene nanoplatelets for the I(3)(-)/I(-) redox reaction are proportional to the concentration of active sites (edge defects and oxidic groups), independent of the electrolyte medium. Dye-sensitized solar cell (DSC) was assembled with this material as a cathode. Semitransparent (>85%) film of graphene nanoplatelets presented no barrier to drain photocurrents at 1 Sun illumination and potentials between 0 and ca. 0.3 V, but an order of magnitude decrease of R(CT) is still needed to improve the behavior of DSC near the open circuit potential and, consequently, the fill factor. We predict that the graphene composite is a strong candidate for replacing both Pt and FTO in cathodes for DSC.

The N ewton‐ X program is a general‐purpose program package for excited‐state molecular dynamics, including nonadiabatic methods. Its modular design allows N ewton‐ X to be easily linked to any quantum‐chemistry package that can provide excited‐state energy gradients. At the current version, N ewton‐ X can perform nonadiabatic dynamics using C olumbus, T urbomole, G aussian, and G amess program packages with multireference configuration interaction, multiconfigurational self‐consistent field, time‐dependent density functional theory, and other methods. Nonadiabatic dynamics simulations with a hybrid combination of methods, such as Quantum‐Mechanics/Molecular‐Mechanics, are also possible. Moreover, N ewton‐ X can be used for the simulation of absorption and emission spectra. The code is distributed free of charge for noncommercial and nonprofit uses at www.newtonx.org . WIREs Comput Mol Sci 2014, 4:26–33. doi: 10.1002/wcms.1158 This article is categorized under: Software > Quantum Chemistry Software > Simulation Methods

Phase-pure TiO2(B) with microfibrous morphology was prepared via a newly developed method from amorphous TiO2. Cyclic voltammetry evidences that Li-insertion into TiO2(B) is governed by a pseudocapacitive faradaic process, whose rate is not limited by solid-state diffusion of Li+ in a broad interval of scan rates. This unusual behavior was discussed in terms of the crystal structure of the TiO2(B) host, having freely accessible parallel channels for Li+-transport perpendicular to the (010) face. The characteristic Li-insertion electrochemistry of TiO2(B) allows re-interpretation of several previous reports, which did not consider explicitly this relation or the presence of TiO2(B) in various TiO2 materials of different origin.