Development of many-body polarizable force fields for Li-battery components: 1. Ether, alkane, and carbonate-based solvents

Classical many-body polarizable force fields were developed for n-alkanes, perflouroalkanes, polyethers, ketones, and linear and cyclic carbonates on the basis of quantum chemistry dimer energies of model compounds and empirical thermodynamic liquid-state properties. The dependence of the electron correlation contribution to the dimer binding energy on basis-set size and level of theory was investigated as a function of molecular separation for a number of alkane, ether, and ketone dimers. Molecular dynamics (MD) simulations of the force fields accurately predicted structural, dynamic, and transport properties of liquids and unentangled polymer melts. On average, gas-phase dimer binding energies predicted with the force field were between those from MP2/aug-cc-pvDz and MP2/aug-cc-pvTz quantum chemistry calculations.     

Amphoteric doping of carbon nanotubes by encapsulation of organic molecules: electronic properties and quantum conductance

In order to investigate and optimize the electronic transport processes in carbon nanotubes doped with organic molecules, we have performed large-scale quantum electronic structure calculations coupled with a Green's function formulation for determining the quantum conductance. Our approach is based on an original scheme where quantum chemistry calculations on finite systems are recast to infinite, non-periodic (i.e., open) systems, therefore mimicking actual working devices. Results from these calculations clearly suggest that the electronic structure of a carbon nanotube can be easily manipulated by encapsulating appropriate organic molecules. Charge transfer processes induced by encapsulated organic molecules lead to efficient n- and p-type doping of the carbon nanotube. Even though a molecule can induce p and n doping, it is shown to have a minor effect on the transport properties of the nanotube as compared to a pristine tube. This type of doping therefore preserves the intrinsic properties of the pristine tube as a ballistic conductor. In addition, the efficient process of charge transfer between the organic molecules and the nanotube is shown to substantially reduce the susceptibility of the pi electrons of the nanotube to modification by oxygen while maintaining stable doping (i.e., no dedoping) at room temperature.     

Will water act as a photocatalyst for cluster phase chemical reactions? Vibrational overtone-induced dehydration reaction of methanediol

The possibility of water catalysis in the vibrational overtone-induced dehydration reaction of methanediol is investigated using ab initio dynamical simulations of small methanediol-water clusters. Quantum chemistry calculations employing clusters with one or two water molecules reveal that the barrier to dehydration is lowered by over 20 kcal/mol because of hydrogen-bonding at the transition state. Nevertheless, the simulations of the reaction dynamics following OH-stretch excitation show little catalytic effect of water and, in some cases, even show an anticatalytic effect. The quantum yield for the dehydration reaction exhibits a delayed threshold effect where reaction does not occur until the photon energy is far above the barrier energy. Unlike thermally induced reactions, it is argued that competition between reaction and the irreversible dissipation of photon energy may be expected to raise the dynamical threshold for the reaction above the transition state energy. It is concluded that quantum chemistry calculations showing barrier lowering are not sufficient to infer water catalysis in photochemical reactions, which instead require dynamical modeling.     

Quantum mechanical investigations of the N(4S)+O2(X 3Sigmag -)-->NO(X 2Pi)+O(3P) reaction

The reaction between energetic nitrogen atoms and oxygen molecules has received important attention in connection with nitric oxide chemistry in the lower thermosphere. We report time-independent quantum mechanical calculations of the N(4S)+O2-->NO+O reaction employing the X 2A' and a 4A' electronic potential energy surfaces of Sayos et al. [J. Chem. Phys. 117, 670 (2002)]. We confirm the production of highly vibrationally excited NO molecules, consistent with previous semiclassical and more recent time-dependent quantum wave packet studies. Calculations are carried out for total angular momentum quantum number J=0 and cross sections and rate coefficients are extracted using the J-shifting approximation. The results are in good agreement with available experimental and theoretical data.     

溴代作用对竹红菌乙素分子性质影响的量子化学研究

用半经验量子化学方法AM1和PM3对竹红菌乙素及其溴代物进行了对比计算,考察了溴代作用对竹红菌乙素分子性质的影响。两种方法所得结果均表明,溴代作用使分子的生成热、前线轨道能级及偶极矩等参数都有所降低,溴代作用也影响了竹红菌乙素分子内氢键的性质,并能使其对光的吸收产生红移。     

Leading RNA tertiary interactions: structures, energies, and water insertion of A-minor and P-interactions. A quantum chemical view

Complex molecular shapes of ribosomal RNA molecules are stabilized by recurrent types of tertiary interactions involving highly specific and conserved non-Watson-Crick base pairs, triplets, and quartets. We analyzed the intrinsic structure and stability of the P-motif and the four basic types of A-minor interactions (types I, II, III, and 0), which represent the most prominent RNA tertiary interaction patterns refined in the course of evolution. In the studied interactions, the electron correlation component of the stabilization usually exceeds the Hartree-Fock (HF) term, leading to a strikingly different balance of forces as compared to standard base pairing stabilized primarily by the HF term. In other words, the A-minor and P-interactions are considerably more influenced by the dispersion energy as compared to canonical base pairs, which makes them particularly suitable to zip the folded RNA structures that are substantially hydrated even in their interior. Continuum solvent COSMO calculations confirm that the stability of the canonical GC base pair is affected (reduced) by the continuum solvent screening considerably more than the stability of the A-minor interaction. Among the studied systems, the strong A-minor II and weak A-minor III interactions require water molecules to stabilize the experimental geometry. Gas-phase optimization of the canonical A-minor II A/CG triplet without water results in a geometry that is clearly inconsistent with the RNA structure. The gas-phase structure of the P-interaction and the most stable A-minor I interaction nicely agrees with the geometries occurring in the ribosome. A-minor I can also adopt an alternative water-mediated substate rather often observed in X-ray and molecular dynamics studies. The A-minor I water bridge, however, does not appear to stabilize the tertiary contact, and its role is to provide structural flexibility to this binding pattern within the context of the RNA structure. Interestingly, the insertion of a polar water molecule in the A-minor I A/CG tertiary contact occurring in the A/C tertiary pair is stabilized primarily by the HF (electrostatic) interaction energy, while the dispersion-controlled A/G contact remains firmly bound. Thus, the intrinsic balance of forces as revealed by quantum mechanics (QM) calculations nicely correlates with many behavioral aspects of the studied interactions inside RNA. The comparison of interaction energies computed using quantum chemistry and an AMBER force field reveals that common molecular mechanics calculations perform rather well, except that the strength of the P-interaction is modestly overestimated. We also briefly discuss the non-negligible methodological differences when evaluating simple base-base nucleic acids base pairs and the complex RNA tertiary base pairing patterns using QM procedures.     

Particle formation and surface processes on atmospheric aerosols: A review of applied quantum chemical calculations

Aerosols significantly influence atmospheric processes such as cloud nucleation, heterogeneous chemistry, and heavy-metal transport in the troposphere. The chemical and physical complexity of atmospheric aerosols results in large uncertainties in their climate and health effects. In this article, we review recent advances in scientific understanding of aerosol processes achieved by the application of quantum chemical calculations. In particular, we emphasize recent work in two areas: new particle formation and heterogeneous processes. Details in quantum chemical methods are provided, elaborating on computational models for prenucleation, secondary organic aerosol formation, and aerosol interface phenomena. Modeling of relative humidity effects, aerosol surfaces, and chemical kinetics of reaction pathways is discussed. Because of their relevance, quantum chemical calculations and field and laboratory experiments are compared. In addition to describing the atmospheric relevance of the computational models, this article also presents future challenges in quantum chemical calculations applied to aerosols.     

Computational study of hydrogen binding by metal-organic framework-5

We report the results of quantum chemistry calculations on H(2) binding by the metal-organic framework-5 (MOF)-5. Density functional theory calculations were used to calculate the atomic positions, lattice constant, and effective atomic charges from the electrostatic potential for the MOF-5 crystal structure. Second-order M?ller-Plesset perturbation theory was used to calculate the binding energy of H(2) to benzene and H(2)-1,4-benzenedicarboxylate-H(2). To achieve the necessary accuracy, the large Dunning basis sets aug-cc-pVTZ, and aug-cc-pVQZ were used, and the results were extrapolated to the basis set limit. The binding energy results were 4.77 kJ/mol for benzene, 5.27 kJ/mol for H(2)-1,4-benzenedicarboxylate-H(2). We also estimate binding of 5.38 kJ/mol for Li-1,4-benzenedicarboxylate-Li and 6.86 kJ/mol at the zinc oxide corners using second-order M?ller-Plesset perturbation theory. In order to compare our theoretical calculations to the experimental hydrogen storage results, grand canonical Monte Carlo calculations were performed. The Monte Carlo simulations identify a high energy binding site at the corners that quickly saturated with 1.27 H(2) molecules at 78 K. At 300 K, a broad range of binding sites are observed.     

Quantum chemistry studies of unbranched fluoropolymers

The results of quantum chemistry calculations of energy and topology parameters, vibration and NMR spectra of model fluorocarbon and unbranched hydrocarbon molecules are presented in this work. The formation of radicals and branches in fluorocarbon molecules and mechanisms of hydrogen substitution by fluorine at fluorination of hydrocarbon paraffins and polymers are discussed based on obtained results.     

Ab-Initio MRD-CI calculations for breaking a chemical bond in a molecule in a crystal or other solid environment. II.H3C—NO2 decomposition of nitromethane in a nitromethane crystal with voids

Recently we extended our strategy for MRD-CI (multireference double excitation-configuration interaction) calculations based on localized/local orbitals and an “effective” CI Hamiltonian for molecular decompositions of large molecules to breaking a chemical bond in a molecule in a crystal or other solid environment. Our technique involves solving a quantum chemical ab-initio SCF explicitly for a system of a reference molecule surrounded by a number of other molecules in the multipole environment of more distant neighbors. The resulting canonical molecular orbitals are then localized and the localized occupied and virtual orbitals in the region of interest are included explicitly in the MRD-CI with the remainder of the occupied localized orbitals being folded into an “effective” CI Hamiltonian. The MRD-CI calculations are carried out for breaking a bond in the reference molecule. This method is completely general. The space treated explicitly quantum chemically and the surrounding space can have voids, defects, deformations, dislocations, impurities, dopants, edges and surfaces, boundaries, etc. We previously applied this procedure successfully to the H₃C? NO₂ bond dissociation of nitromethane in a nitromethane crystal with extensive testing of the number of molecules that have to be included explicitly in the SCF and how many molecules have to be represented by more distant multipoles. The results indicated that it took more energy to dissociate the H₃C? NO₂ bond when the nitromethane molecule was in the crystal than it did to dissociate that bond in the free nitromethane molecule. In this present study we have investigated the effect of voids (both in the nitromethane molecules treated explicitly in the SCF and those in the environment represented by multipoles) on the calculated H₃C? NO₂ bond dissociation energies.     

Real‐time quantum chemistry

Significant progress in the development of efficient and fast algorithms for quantum chemical calculations has been made in the past two decades. The main focus has always been the desire to be able to treat ever larger molecules or molecular assemblies—especially linear and sublinear scaling techniques are devoted to the accomplishment of this goal. However, as many chemical reactions are rather local, they usually involve only a limited number of atoms so that models of about 200 (or even less) atoms embedded in a suitable environment are sufficient to study their mechanisms. Thus, the system size does not need to be enlarged, but remains constant for reactions of this type that can be described by less than 200 atoms. The question then arises how fast one can obtain the quantum chemical results. This question is not directly answered by linear‐scaling techniques. In fact, ideas such as haptic quantum chemistry (HQC) or interactive quantum chemistry require an immediate provision of quantum chemical information which demands the calculation of data in “real time.” In this perspective, we aim at a definition of real‐time quantum chemistry, explore its realm and eventually discuss applications in the field of HQC. For the latter, we elaborate whether a direct approach is possible by virtue of real‐time quantum chemistry. © 2012 Wiley Periodicals, Inc.     

A Classical and Quantum Chemical Analysis of Gaseous Heat Capacity

Physical chemistry is considered to be a scientifically abstract and mathematically intensive course in the undergraduate chemistry curriculum. To most students, the physical chemistry course involves a semester that deals with macroscopic properties and another that deals with microscopic evaluations of chemical systems. They often fail to see the importance of statistical mechanics in making the connection between the content of the two semesters. In this paper, we propose a computational exercise that complements a simple physical chemistry experiment that can be used to understand the chemical basis of a macroscopic property such as the heat capacity of gases using microscopic (classical and quantum) mechanics. Students are given the opportunity to use (1) computational chemistry software to calculate the contributions of translational, rotational, and vibrational motion to the energy of molecules; (2) a graphing program to study the linear and nonlinear dependence of energy on temperature; (3) classical, quantum, and statistical mechanical theory to verify experimental data; (4) regression analysis to approximate the heat capacity constant of simple gases from energy calculations.     

Computational Chemistry to the Rescue: Modern Toolboxes for the Assignment of Complex Molecules by GIAO NMR Calculations

The calculations of NMR properties of molecules using quantum chemical methods have deeply impacted several branches of organic chemistry. They are particularly important in structural or stereochemical assignments of organic compounds, with implications in total synthesis, stereoselective reactions, and natural products chemistry. In studying the evolution of the strategies developed to support (or reject) a structural proposal, it becomes clear that the most effective and accurate ones involve sophisticated procedures to correlate experimental and computational data. Owing to their relatively high mathematical complexity, such calculations (CP3, DP4, ANN‐PRA) are often carried out using additional computational resources provided by the authors (such as applets or Excel files). This Minireview will cover the state‐of‐the‐art of these toolboxes in the assignment of organic molecules, including mathematical definitions, updates, and discussion of relevant examples.     

Water catalysis and anticatalysis in photochemical reactions: observation of a delayed threshold effect in the reaction quantum yield

The possible catalysis of photochemical reactions by water molecules is considered. Using theoretical simulations, we investigate the HF-elimination reaction of fluoromethanol in small water clusters initiated by the overtone excitation of the hydroxyl group. The reaction occurs in competition with the process of water evaporation that dissipates the excitation and quenches the reaction. Although the transition state barrier is stabilized by over 20 kcal/mol through hydrogen bonding with water, the quantum yield versus energy shows a pronounced delayed threshold that effectively eliminates the catalytic effect. It is concluded that the quantum chemistry calculations of barrier lowering are not sufficient to infer water catalysis in some photochemical reactions, which instead require dynamical modeling.     

Exploiting graphical processing units to enable quantum chemistry calculation of large solvated molecules with conductor-like polarizable continuum models

The conductor-like polarizable continuum model (C-PCM) with switching/Gaussian smooth discretization is a widely used implicit solvation model in quantum chemistry. We have previously implemented C-PCM solvation for Hartree-Fock (HF) and density functional theory (DFT) on graphical processing units (GPUs), enabling the quantum mechanical treatment of large solvated biomolecules. Here, we first propose a GPU-based algorithm for the PCM conjugate gradient linear solver that greatly improves the performance for very large molecules. The overhead for PCM-related evaluations now consumes less than 15% of the total runtime for DFT calculations on large molecules. Second, we demonstrate that our algorithms tailored for ground state C-PCM are transferable to excited state properties. Using a single GPU, our method evaluates the analytic gradient of the linear response PCM time-dependent density functional theory energy up to 80× faster than a conventional central processing unit (CPU)-based implementation. In addition, our C-PCM algorithms are transferable to other methods that require electrostatic potential (ESP) evaluations. For example, we achieve speed-ups of up to 130× for restricted ESP-based atomic charge evaluations, when compared to CPU-based codes. We also summarize and compare the different PCM cavity discretization schemes used in some popular quantum chemistry packages as a reference for both users and developers.     

Evaluation of the field-adapted ADMA approach: absolute and relative energies of crambin and derivatives

A large number of conformations and chemically modified variants of the protein crambin were used to extensively test the field-adapted adjustable density matrix assembler (FA-ADMA) method developed for ab initio quality quantum chemistry computations of proteins and other macromolecules, introduced in an earlier publication. In this method, the fuzzy density matrix fragmentation scheme of the original adjustable density matrix assembler (ADMA) method has been made more efficient by combining it with an approach of using point charges to approximate the effects of additional, distant parts of a given macromolecule in the quantum chemical calculation of each fragment. In this way, smaller parent molecules can be used for fragment generation, while achieving accuracy that can be obtained only with large parent molecules in the original ADMA method. Whereas in both methods the error relative to the Hartree-Fock result can be reduced below any threshold by choosing large enough parent molecules, this can be done more efficiently with the new method. In order to obtain reliable test results for the accuracy obtainable by the new method when compared to conventional Hartree-Fock calculations, we performed a large number of energy calculations for the protein crambin using various conformations available in the Protein Data Bank, various protonation states, and side chain mutations. Additionally, in order to test the performance of the method for protein-solvent interaction studies, the energy changes due to the formation of complexes with ethanol and single and multiple water molecules were investigated.     

The impact of the nucleoside oxidation on the susceptibility to chemical carcinogens studied by first principle and semiempirical quantum chemistry methods

The B3LYP/aug-cc-pvdz and AM1-CI quantum chemistry calculations were used for estimation of adiabatic and vertical ionization potential values of 22 hydroxyl radical modified purine and pyrimidine model nucleosides. Most of studied derivatives are characterized by higher values of IP compared to canonical guanosine, which is known to be the main target for oxidizing agents and chemical carcinogens in cellular DNA. However, three derivatives, namely fapy-guanosine, 8-oxoguanosine and 2-oxoadenosine are characterized by lower IP values than canonical guanosine. Thus, 6,8-diketo- and 6-enol-8-keto-tautomer of 8-oxoguanosine, 6-enol- and 6-keto tautomers of fapy-guanosine as well as 2-keto form of 2-oxoadenosine may be potential hot spot centers for chemical carcinogens. The IEFPCM calculations confirm above conclusion even in the polar environment.     

Franck–Condon Blockade and Aggregation‐Modulated Conductance in Molecular Devices Using Aggregation‐Induced Emission‐Active Molecules

We report an effective modulation of the quantum transport in molecular junctions consisting of aggregation‐induced‐emission(AIE)‐active molecules. Theoretical simulations based on combined density functional theory and rate‐equation method calculations show that the low‐bias conductance of the junction with a single tetraphenylethylene (TPE) molecule can be completely suppressed by strong electron–vibration couplings, that is, the Franck‐Condon blockade effect. It is mainly associated with the low‐energy vibration modes, which is also the origin of the fluorescence quenching of the AIE molecule in solution. We further found that the conductance of the junction can be lifted by restraining the internal motion of the TPE molecule by either methyl substitution on the phenyl group or by aggregation, a mechanism similar to the AIE process. The present work demonstrates the correlation between optical processes of molecules and quantum transport in their junction, and thus opens up a new avenue for the application of AIE‐type molecules in molecular electronics and functional devices.     

Use of Electron-Density Plots in Applied Quantum Chemistry

The uses in applied quantum chemistry of computer-produced three-dimensional diagrams of electron-density distributions are discussed. The two major catagories of such diagrams are contrasted; and advantages are described for plots showing as the third dimension the point-by-point electron density in a cross-sectional cut (corresponding to the other two dimensions) through a molecule. Examples are presented to show how these plots may be used (1) to assess the adequacies of a given mathematical representation employed in the calculation of a wavefunction, (2) to clarify the interrelationship between an individual molecular orbital and the atomic orbitals of the constituent atoms, as well as (3) to explain the canonical set of molecular orbitals of any selected molecule. Furthermore these plots serve(4) to demonstrate clearly a replication of key characteristics between certain molecular orbitals in different molecules. These examples are accompanied by others which indicate how the electron-density plots may be used(5) to understand and clarify accepted chemical dogma. Finally, the possibility is discussed of employing quantum calculations on a wider scale so as to be of value in the more practical aspects of chemistry.     

Theoretically Rational Designs of Transport Organic Semiconductors Based on Heteroacenes

A Marcus electron transfer theory coupled with an incoherent polaron hopping and charge diffusion model in combining with first‐principle quantum chemistry calculation was applied to investigating the effects of heteroatom on the intermolecular charge transfer rate for a series of heteroacene molecules. The influences of intermolecular packing and charge reorganization energy were discussed. It was found that the sulphur and nitrogen substituted heteroacenes were intrinsically hole‐transporting materials due to the reduced hole reorganization energy and the enhanced overlap between HOMOs. For the oxygen‐substituted heteroacene, it was found that both the electronic couplings and the reorganization energies for holes and electrons were comparative, indicating the application potential of ambipolar devices. Most interestingly, for the boron‐substituted heteroacenes, theoretical calculations predicted a promising electron‐transport material, which is rare for organic materials. These findings provide insights into rationally designing organic semiconductors with specific properties.