Quantum Chemical Potential Energy Surface Research Articles

Simple Physical Model for the Estimation of Irreversible Dissociation Rates for Bimolecular Complexes.

In this article, we propose a simple method of estimating dissociation rates of bimolecular van der Waals complexes ("wells"), rooted in rigid body dynamics, requiring as input parameters only the bimolecular binding energy, together with the intermolecular equilibrium distance and moments of inertia of the complex. The classical equations of motion are solved for the intermolecular and rotational degrees of freedom in a coordinate system considering only the relative motion of the two molecules, thus bypassing the question of whether the energy of the complex is statistically distributed. Well-escaping trajectories are modeled from these equations, and the escape rate as a function of relative velocity and angular momentum is fitted to an empirical function, which is then integrated over a probability distribution of said quantities. By necessity, this approach makes crude assumptions on the shape of the potential well and neglects the impact of energy quantization, and, more crucially, the coupling between the degrees of freedom included in the equations of motion with those that are not. We quantify the error caused by the first assumption by comparing our model potential with a quantum chemical potential energy surface (PES) and show that while the model does make several compromises and may not be accurate for all classes of bimolecular complexes, it is able to produce physically consistent dissociation rate coefficients within typical atmospheric chemistry confidence intervals for triplet state alkoxyl radical complexes, for which the detailed balance approach has been shown to fail.

VIB5 database with accurate ab initio quantum chemical molecular potential energy surfaces

High-level ab initio quantum chemical (QC) molecular potential energy surfaces (PESs) are crucial for accurately simulating molecular rotation-vibration spectra. Machine learning (ML) can help alleviate the cost of constructing such PESs, but requires access to the original ab initio PES data, namely potential energies computed on high-density grids of nuclear geometries. In this work, we present a new structured PES database called VIB5, which contains high-quality ab initio data on 5 small polyatomic molecules of astrophysical significance (CH3Cl, CH4, SiH4, CH3F, and NaOH). The VIB5 database is based on previously used PESs, which, however, are either publicly unavailable or lacking key information to make them suitable for ML applications. The VIB5 database provides tens of thousands of grid points for each molecule with theoretical best estimates of potential energies along with their constituent energy correction terms and a data-extraction script. In addition, new complementary QC calculations of energies and energy gradients have been performed to provide a consistent database, which, e.g., can be used for gradient-based ML methods.

Picosecond excited-state lifetimes of protonated indazole and benzimidazole: The role of the N-N bond.

Certain chemical groups give rise to characteristic excited-state deactivation mechanisms. Here, we target the role of a protonated N-N chemical group in the excited-state deactivation of protonated indazole by comparison to its isomer that lacks this group, protonated benzimidazole. Gas-phase protonated indazole and protonated benzimidazole ions are investigated at room temperature using picosecond laser pump-probe photodissociation experiments in a linear ion-trap. Excited state lifetimes are measured across a range of pump energies (4.0-5.4eV). The 1ππ* lifetimes of protonated indazole range from 390 ± 70ps using 4.0eV pump energy to ≤18ps using 4.6eV pump energy. The 1ππ* lifetimes of protonated benzimidazole are systematically longer, ranging from 3700 ± 1100ps at 4.6eV pump energy to 400 ± 200ps at 5.4eV. Based on these experimental results and accompanying quantum chemical calculations and potential energy surfaces, the shorter lifetimes of protonated indazole are attributed to πσ* state mediated elongation of the protonated N-N bond.

Fitting quantum machine learning potentials to experimental free energy data: predicting tautomer ratios in solution.

The computation of tautomer ratios of druglike molecules is enormously important in computer-aided drug discovery, as over a quarter of all approved drugs can populate multiple tautomeric species in solution. Unfortunately, accurate calculations of aqueous tautomer ratios—the degree to which these species must be penalized in order to correctly account for tautomers in modeling binding for computer-aided drug discovery—is surprisingly difficult. While quantum chemical approaches to computing aqueous tautomer ratios using continuum solvent models and rigid-rotor harmonic-oscillator thermochemistry are currently state of the art, these methods are still surprisingly inaccurate despite their enormous computational expense. Here, we show that a major source of this inaccuracy lies in the breakdown of the standard approach to accounting for quantum chemical thermochemistry using rigid rotor harmonic oscillator (RRHO) approximations, which are frustrated by the complex conformational landscape introduced by the migration of double bonds, creation of stereocenters, and introduction of multiple conformations separated by low energetic barriers induced by migration of a single proton. Using quantum machine learning (QML) methods that allow us to compute potential energies with quantum chemical accuracy at a fraction of the cost, we show how rigorous relative alchemical free energy calculations can be used to compute tautomer ratios in vacuum free from the limitations introduced by RRHO approximations. Furthermore, since the parameters of QML methods are tunable, we show how we can train these models to correct limitations in the underlying learned quantum chemical potential energy surface using free energies, enabling these methods to learn to generalize tautomer free energies across a broader range of predictions.

High performance global exploration of isomers and isomerization channels on quantum chemical potential energy surface of H5 C2 NO2.

High performance global exploration of isomers and isomerization channels on the quantum chemical potential energy surface (PES) is performed for H5 C2 NO2 by using the scaled hypersphere search-anharmonic downward distortion following (SHS-ADDF) method. A multi-node operation, NeoGRRM, has achieved high performance exploration calculations for the large system by submitting SHS-ADDF sub-jobs into many cores in parallel and unifying the results of sub-jobs into the total lists of the main-job. Global exploration of equilibrium (EQ) and transition-state structures at the level of B3LYP/6-31G(d) gave 3210 EQs and 23278 TSs. Nine compounds were found in the low energy regions of 0-100 kJ/mol; the lowest energy compound is N-methylcarbamic acid, the second is methyl carbamate, and the third is glycine (the most fundamental amino acid). Interconversion pathways between the conformers of each of the low energy compounds were surveyed. Isomerization channels around glycine were explored in detail. The lowest energy barriers around some of the EQs turned to be negative after zero-point energy corrections. This indicates that those structures cannot exist as independent structures because they spontaneously collapse into more stable structures. The global PES search showed various interesting dissociating channels which indicate synthon reaction pathways in the reverse directions.

Isomer-selected ion-molecule reactions of acetylene cations with propyne and allene.

One of the fundamental goals of chemistry is to determine how molecular structure influences interactions and leads to different reaction products. Studies of isomer-selected and resolved chemical reactions can shed light directly on how form leads to function. In the following, we present the results of gas-phase reactions between acetylene cations (C2D2+) with two different isomers of C3H4: propyne (DC3D3) and allene (H2C3H2). Our highly controlled, trapped-ion environment allows for precise determination of reaction products and kinetics. From these results, we can infer details of the underlying reaction dynamics of C2H2+ + C3H4. Through the synergy of experimental results and high-level quantum chemical potential energy surface calculations, we are able to identify distinct reaction mechanisms for the two isomers. We find long-range charge exchange with no complex formation is favored for allene, whereas charge exchange leads to an intermediate reaction complex for propyne and thus, different products. Therefore, this reaction displays a pronounced isomer-selective bi-molecular reactive process.

Spectroscopic and thermal properties of stannadithiane compounds bearing endocyclic ether and lactone groups.

Four related stannadithiane compounds containing different endocyclic functional groups -including ether (1), diether (2), lactone (3), and spirolactone (4)- were prepared. The conformational landscape has been fully determined for the 8-membered representative (compound 1) resulting in a distorted crown form with the butyl chains adopting an extended conformation. The infrared and Raman spectra of stannadithiane species have been measured and interpreted, aided by quantum chemical calculations and potential energy surface analysis. Special attention has been devoted to the analysis of the vibrational features of the heterocyclic moieties. The characteristic νas(SnS) and νs(SnS) stretching modes of the SnS2endo-cyclic group were clearly observed in the Raman spectra at around 340 and 315 cm-1, respectively. The exo-cyclic ν(SnC) stretching modes were found near 590 and 565 cm-1 for the antisymmetric and symmetric motions, respectively. Thermal behavior for compounds 2-4 has been determined by thermogravimetric methods.

Exploration of Carbon Allotropes with Four-membered Ring Structures on Quantum Chemical Potential Energy Surfaces.

The existence of a new carbon allotrope family with four-membered rings as a key unit has been recently predicted with quantum chemical calculations. This family includes carbon allotropes in prism-, polymerized prism-, sheet-, tube-, and wavy-forms. An atypical bond property has been observed in this series of carbon structures, which differs from the typical sp3 , sp2 , and sp hybridizations. The lowest energy barrier from some of the equilibrium states of the carbon structures has been determined with the SHS-ADDF (scaled-hypersphere-search combined with the anharmonic downward distortion following) method within the GRRM software program package. The height of the barriers indicates that the well is deep enough for the carbon structures to exist. This class of carbon allotropes is expected to be energy-reservoirs with extra energy of 100-350 kJ mol-1 per one carbon atom. This article presents the structures, energies and reactivity of the carbon allotropes with four-membered ring structures as well as the background of the findings in the context of the global exploration of potential energy surfaces. © 2018 Wiley Periodicals, Inc.

Quantum chemical exploration of formaldehyde clusters (H2 CO)n (n = 2-4).

Global exploration of equilibrium structures and interconversion pathways on the quantum chemical potential energy surface (PES) is performed for (H2 CO)n (n = 2-4) by using the Scaled Hypersphere Search-Anharmonic Downward Distortion Following (SHS-ADDF) method. Density functional theoretical (DFT) calculations with empirical dispersion corrections (D3) yielded comparable results for formaldehyde dimer in comparison with recent detailed studies at CCSD(T) levels. Based on DFT-D3 calculations, trimer and tetramer structures and their stabilities were studied. For tetramer, a highly symmetrical S4 structure was found as the most stable form in good accordance with experimentally determined tetramer unit in the formaldehyde crystal. © 2018 Wiley Periodicals, Inc.

Measurement of reaction rate constants using RCM: A case study of decomposition of dimethyl carbonate to dimethyl ether

This paper proposes a method to measure the reaction rate constants in kinetically-simple pyrolysis systems using rapid compression machine (RCM) and fast sampling. The method involves first performing sensitivity analysis based on a reasonable kinetic model to identify the species dominated by a target reaction. Then the time-resolved species concentration profiles are measured in RCM experiments using fast sampling and gas chromatography. Finally, the pre-assigned pre-exponential factor and the activation energy are optimized by an iterative fitting procedure, in which the entire temperature profile derived from the pressure history is taken into account. In order to validate this method, the rate constant of the reaction CH3OCHO (methyl formate, MF) => CH3OH+CO (R1) was determined by measuring the CO concentration over 948–1112K at 30bar, obtaining the rate expressionkR1/s−1=3.04×1013exp(−30968K/T), which is consistent with previous theoretical and experimental studies. The rate constant of the reaction CH3OCOOCH3 (dimethyl carbonate, DMC) => CH3OCH3 (dimethyl ether, DME)+CO2 (R2) was then studied by measuring the time-resolved DME concentration over 994–1068K at 30bar. The measured rate expression of kR2/s−1=2.02×1013exp(−34248K/T)with an uncertainty of ±30% agrees well with the RRKM/Master Equation calculation based on a high-level quantum chemical potential energy surface.

Global exploration of isomers and isomerization channels on the quantum chemical potential energy surface of H3 CNO3.

Global exploration of isomers and isomerization channels on the quantum chemical potential energy surface (PES) is performed for H3 CNO3 using the Scaled Hypersphere Search-Anharmonic Downward Distortion Following (SHS-ADDF) method. The molecular formula of H3 CNO3 includes functional groups of CH3 , OH, NH2 , COOH, NO, NO2 , and NO3 , which are very important in connection with amino acids and NOx. Geometrical structures and interconversion pathways are disclosed after 18719781 force calculations and 534726 Hessian calculations at the level of B3LYP/6-31G(d). The explored results are confirmed to be valid, especially for the important lower energy regions, by re-optimization at the higher level of B3LYP/6-311++G(d,p). A global reaction route-mapping using SHS-ADDF demonstrates the entire view and undeveloped landscapes on PES of H3 CNO3 . Typical compounds of H3 CNO3 , aminoxy formic acid, hydroxycarbamic acid, aminoperformic acid, hydroxymethyl nitrite, nitromethanol, methyl nitrate, methyl peroxynitrite, and dioxaziridine, are well separated from others by very high energy-barriers. The stable-most conformer of H3 CNO3 is difficult to be determined, because of seven structures existing with nearly the same energies within 5.7 kJ/mol at the level of CCSD(T)/aug-cc-pVTZ. © 2017 Wiley Periodicals, Inc.

Artificial Force Induced Reaction (AFIR) Method for Exploring Quantum Chemical Potential Energy Surfaces.

In this account, a technical overview of the artificial force induced reaction (AFIR) method is presented. The AFIR method is one of the automated reaction-path search methods developed by the authors, and has been applied extensively to a variety of chemical reactions, such as organocatalysis, organometallic catalysis, and photoreactions. There are two modes in the AFIR method, i.e., a multicomponent mode and a single-component mode. The former has been applied to bimolecular and multicomponent reactions and the latter to unimolecular isomerization and dissociation reactions. Five numerical examples are presented for an Aldol reaction, a Claisen rearrangement, a Co-catalyzed hydroformylation, a fullerene structure search, and a nonradiative decay path search in an electronically excited naphthalene molecule. Finally, possible applications of the AFIR method are discussed.

Anharmonic Downward Distortion Following for Automated Exploration of Quantum Chemical Potential Energy Surfaces

Abstract This article gives a comprehensive review of the anharmonic downward distortion following (ADDF) method. The ADDF method has been developed as an automated reaction path search method. This method follows the anharmonic downward distortion (ADD) toward transition states and dissociation channels starting from a local minimum on the potential energy surface (PES). Systematic applications of the ADDF method to all local minima provide a global network of reaction pathways on the PES of given chemical formulas. Various extensions have been proposed and applied to many interesting chemical problems such as elucidation of photodissociation mechanisms, structure prediction of H-bonded clusters, mechanistic studies of organometallic catalysis, design of generation–conversion routes of amino acid molecules, and so on. It has also been employed in efficient construction of anharmonic PESs for highly accurate vibrational analysis. These developments and applications are illustrated with some representative results.

Roads leading to roam. Role of triple fragmentation and of conical intersections in photochemical reactions: experiments and theory on methyl formate

The exploration of alternative roads that open to molecules with sufficient energy to yield different products permits prediction and eventually control of the outcomes of chemical reactions. Advanced imaging techniques for monitoring laser-induced photodissociation are here combined with dynamical simulations, involving ample sets of classical trajectories generated on a quantum chemical potential energy surface. Methyl formate, HCOOCH3, is photodissociated at energies near the triple fragmentation threshold into H, CO and OCH3. Images of velocity and rotational distributions of CO exhibit signatures of alternative routes, such as those recently designated as transition-state vs. roaming-mediated. Furthermore, a demonstration of the triple fragmentation route is given, and also confirmed by H-atom product imaging and FTIR time-resolved spectra of the intermediate HCO radical. In addition, the relevance of nonadiabatic transitions promoted by a conical intersection is clarified by simulations as the privileged "reactivity funnel" of organic photochemistry, whereby the outcomes of molecular photoexcitation are delivered to electronic ground states.

Thermally induced polarizabilities and dipole moments of small tin clusters

We study the influence of thermal excitation on the electric susceptibilities for Sn(6) and Sn(7) clusters by molecular beam electric deflection and Monte-Carlo simulations in conjunction with quantum-chemical calculations. At low temperatures (40 K), no field-induced broadening of the Sn(6) and Sn(7) cluster beams are observed, in agreement with vanishing permanent electric dipole moments due to their centro-symmetrical ground states. The electric polarizabilities of Sn(6) and Sn(7), as inferred from the field-induced molecular beam deflection, are in good agreement with the quantum-chemical predictions. At elevated temperatures of 50-100 K, increased polarizabilities of about 2-3 Å(3) are obtained. Also, we found indications of a field-induced beam broadening which points to the existence of permanent dipole moments of about 0.01-0.02 D per atom at higher temperatures. These results cannot be explained by thermal excitations within a harmonic oscillator model, which would yield a temperature-independent polarizability and fluxional, but not permanent, dipole moments. We analyze this behavior by Monte-Carlo simulations in order to compute average temperature-induced electric dipole moments. For that purpose, we developed a novel technique for predicting observables sampled on the quantum-chemical potential energy surface by an umbrella sampling correction of Monte-Carlo results obtained from simulations utilizing an empirical potential. The calculated, fluxional dipole moments are in tune with the observed beam broadenings. The cluster dynamics underlying the polarizability appear to be intermediate between rigid and floppy molecules which leads to the conclusion that the rotational, not the vibrational temperature seems to be the key parameter that determines the temperature dependence of the polarizability.

Quantum Chemical Prediction of Reaction Pathways and Rate Constants for the Reactions of Ox (x = 1 and 2) with Pristine and Defective Graphite (0001) Surfaces

We present reaction pathways for adsorption reactions of the O atom and O2 molecule in the pristine and monovacancy defective graphite (0001) based on quantum chemical potential energy surfaces (PESs) obtained by the dispersion-augmented density-functional tight-binding (DFTB-D) method. We use a dicircumcoronene C96H24 (L0D) graphene slab as the pristine graphite (0001) model and dicircumcoronene C95H24 (LIV) as the graphite (0001) monovacancy defect model. We found that the adsorption reactions of O and O2 on the L0D surface can produce defects on the graphite surface. O can yield CO, while O2 can yield both CO and CO2 molecules. The adsorption reactions of the O and O2 on the LIV surface can produce a 2-C defective graphite surface and CO, and CO and CO2, respectively. The O and O2 more readily oxidize the defected surface, LIV, than the defect-free surface, L0D. On the basis of the computed reaction pathways, we predict reaction rate constants in the temperature range between 300 and 3000 K using Rice–Ramsperger–Kassel–Marcus (RRKM) theory. High-temperature quantum chemical molecular dynamics simulations at 3000 K based on on-the-fly DFTB-D energies and gradients support the results of our PES studies.

Finding Reaction Pathways of Type A + B → X: Toward Systematic Prediction of Reaction Mechanisms

In these five decades, many useful tools have been developed for exploring quantum chemical potential energy surfaces. The success in theoretical studies of chemical reaction mechanisms has been greatly supported by these tools. However, systematic prediction of reaction mechanisms starting only from given reactants and catalysts is still very difficult. Toward this goal, we describe the artificial force induced reaction (AFIR) method for automatically finding reaction paths of type A + B → X (+ Y). By imposing an artificial force to given reactants and catalysts, the method can find the reactive sites very efficiently. Further pressing by the artificial force provides approximate transition states and product structures, which can be easily reoptimized to the corresponding true ones. This procedure can be executed very efficiently just by minimizing a single function called the AFIR function. All important reaction paths can be found by repeating this cycle starting from many initial orientations. We also discuss perspectives of automated reaction path search methods toward the above goal.

Quantum Chemical Prediction of Reaction Pathways and Rate Constants for Reactions of NO and NO2 with Monovacancy Defects on Graphite (0001) Surfaces

We present reaction pathways for adsorption reactions of NO and NO2 molecules in the vicinity of monovacancy defects on graphite (0001) based on quantum chemical potential energy surfaces (PESs) obtained by B3LYP and dispersion-augmented density-functional tight-binding (DFTB-D) methods. To model the graphite (0001) monovacancy defects, finite-size molecular model systems up to the size of dicircumcoronene (C95H24) were employed. We find that the reactions of NOx on the monodefective graphite surface are initiated by rapid association processes with negligible barriers, leading to nitridation and oxidation of the graphite surface, and eventually producing gaseous COx, NO, and CN species leaving from an even more defective graphite surface. On the basis of the computed reaction pathways, we predict reaction rate constants in the temperature range between 300 and 3000 K using Rice−Ramsperger−Kassel−Marcus theory. High-temperature quantum chemical molecular dynamics simulations at 3000 K based on on-the-fly DFTB-D energies and gradients support the results of our PES studies.

Development of glycyl radical parameters for the OPLS-AA/L force field

On the basis of quantum chemical calculations C(alpha)-glycyl radical parameters have been developed for the OPLS-AA/L force field. The molecular mechanics hypersurface was fitted to the calculated quantum chemical surface by minimizing their molecular mechanics parameter dependent sum-of-squares deviations. To do this, a computer program in which the molecular mechanics energy derivatives with respect to the parameters were calculated analytically was developed, implementing the general method of Lifson and Warshel (J Chem Phys 1968, 49, 5116) for force field parameter optimization. This program, in principle, can determine the optimal parameter set in one calculation if enough representative value points on the quantum chemical potential energy surface are available and there is no linear dependency between the parameters. Some of the parameters in quantum calculations, including several new torsion types around a bond as well as angle parameters at a new central atom type, are not completely separable. Consequently, some restrictions and/or presumptions were necessary during parameter optimization. The relative OPLS-AA energies reproduced those calculated quantum chemically almost perfectly.

Efficient methods for finding transition states in chemical reactions: Comparison of improved dimer method and partitioned rational function optimization method

A combination of interpolation methods and local saddle-point search algorithms is probably the most efficient way of finding transition states in chemical reactions. Interpolation methods such as the growing-string method and the nudged-elastic band are able to find an approximation to the minimum-energy pathway and thereby provide a good initial guess for a transition state and imaginary mode connecting both reactant and product states. Since interpolation methods employ usually just a small number of configurations and converge slowly close to the minimum-energy pathway, local methods such as partitioned rational function optimization methods using either exact or approximate Hessians or minimum-mode-following methods such as the dimer or the Lanczos method have to be used to converge to the transition state. A modification to the original dimer method proposed by [Henkelman and Jonnson J. Chem. Phys. 111, 7010 (1999)] is presented, reducing the number of gradient calculations per cycle from six to four gradients or three gradients and one energy, and significantly improves the overall performance of the algorithm on quantum-chemical potential-energy surfaces, where forces are subject to numerical noise. A comparison is made between the dimer methods and the well-established partitioned rational function optimization methods for finding transition states after the use of interpolation methods. Results for 24 different small- to medium-sized chemical reactions covering a wide range of structural types demonstrate that the improved dimer method is an efficient alternative saddle-point search algorithm on medium-sized to large systems and is often even able to find transition states when partitioned rational function optimization methods fail to converge.