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Arindam Chakraborty

Publications and source records attributed to Arindam Chakraborty.

9 recordsLinked to original sources

Explicit dynamical electron-proton correlation in the nuclear-electronic orbital framework.

A method that includes explicit electron-proton correlation directly into the nuclear-electronic orbital self-consistent-field framework is presented. This nuclear-electronic orbital explicitly correlated Hartree-Fock (NEO-XCHF) scheme is formulated using Gaussian basis functions for the electrons and the quantum nuclei in conjunction with Gaussian-type geminal functions. The NEO approach is designed for the quantum treatment of a relatively small number of nuclei, such as the hydrogen nuclei involved in key hydrogen bonding interactions or hydrogen transfer reactions. The conventional nuclear-electronic-orbital-based methods produce nuclear wave functions that are too localized, leading to severe overestimations of hydrogen vibrational frequencies, as well as inaccuracies in geometries, isotope effects, couplings, and tunneling splittings. The application of the NEO-XCHF approach to a model system illustrates that the description of the nuclear wave function is significantly improved by the inclusion of explicit electron-proton correlation. In contrast to the NEO-HF method, the NEO-XCHF method leads to hydrogen vibrational stretch frequencies that are in excellent agreement with those calculated from grid-based methods. This approach is computationally practical for many-electron systems because only a relatively small number of nuclei are treated quantum mechanically and only electron-proton correlation is treated explicitly. Electron-electron dynamical correlation can be included with density functional theory or perturbation theory methods.

Letter↗

Converged vibrational energy levels and quantum mechanical vibrational partition function of ethane.

The vibrational partition function of ethane is calculated in the temperature range of 200-600 K using well-converged energy levels that were calculated by vibrational configuration interaction, and the results are compared to the harmonic oscillator partition function. This provides the first test of the harmonic oscillator approximation for a molecule with more than five atoms. The absolute free energies computed by the harmonic oscillator approximation are in error by 0.59-0.62 kcal/mol over the 200-600 K temperature range.

Journal Article↗

Combined valence bond-molecular mechanics potential-energy surface and direct dynamics study of rate constants and kinetic isotope effects for the H + C2H6 reaction.

This article presents a multifaceted study of the reaction H+C(2)H(6)-->H(2)+C(2)H(5) and three of its deuterium-substituted isotopologs. First we present high-level electronic structure calculations by the W1, G3SX, MCG3-MPWB, CBS-APNO, and MC-QCISD/3 methods that lead to a best estimate of the barrier height of 11.8+/-0.5 kcal/mol. Then we obtain a specific reaction parameter for the MPW density functional in order that it reproduces the best estimate of the barrier height; this yields the MPW54 functional. The MPW54 functional, as well as the MPW60 functional that was previously parametrized for the H+CH(4) reaction, is used with canonical variational theory with small-curvature tunneling to calculate the rate constants for all four ethane reactions from 200 to 2000 K. The final MPW54 calculations are based on curvilinear-coordinate generalized-normal-mode analysis along the reaction path, and they include scaled frequencies and an anharmonic C-C bond torsion. They agree with experiment within 31% for 467-826 K except for a 38% deviation at 748 K; the results for the isotopologs are predictions since these rate constants have never been measured. The kinetic isotope effects (KIEs) are analyzed to reveal the contributions from subsets of vibrational partition functions and from tunneling, which conspire to yield a nonmonotonic temperature dependence for one of the KIEs. The stationary points and reaction-path potential of the MPW54 potential-energy surface are then used to parametrize a new kind of analytical potential-energy surface that combines a semiempirical valence bond formalism for the reactive part of the molecule with a standard molecular mechanics force field for the rest; this may be considered to be either an extension of molecular mechanics to treat a reactive potential-energy surface or a new kind of combined quantum-mechanical/molecular mechanical (QM/MM) method in which the QM part is semiempirical valence bond theory; that is, the new potential-energy surface is a combined valence bond molecular mechanics (CVBMM) surface. Rate constants calculated with the CVBMM surface agree with the MPW54 rate constants within 12% for 534-2000 K and within 23% for 200-491 K. The full CVBMM potential-energy surface is now available for use in variety of dynamics calculations, and it provides a prototype for developing CVBMM potential-energy surfaces for other reactions.

Journal Article↗

Quantum mechanical reaction rate constants by vibrational configuration interaction: the OH + H2->H2O + H reaction as a function of temperature.

The thermal rate constant of the 3D OH + H(2)-->H(2)O + H reaction was computed by using the flux autocorrelation function, with a time-independent square-integrable basis set. Two modes that actively participate in bond making and bond breaking were treated by using 2D distributed Gaussian functions, and the remaining (nonreactive) modes were treated by using harmonic oscillator functions. The finite-basis eigenvalues and eigenvectors of the Hamiltonian were obtained by solving the resulting generalized eigenvalue equation, and the flux autocorrelation function for a dividing surface optimized in reduced-dimensionality calculations was represented in the basis formed by the eigenvectors of the Hamiltonian. The rate constant was obtained by integrating the flux autocorrelation function. The choice of the final time to which the integration is carried was determined by a plateau criterion. The potential energy surface was from Wu, Schatz, Lendvay, Fang, and Harding (WSLFH). We also studied the collinear H + H(2) reaction by using the Liu-Siegbahn-Truhlar-Horowitz (LSTH) potential energy surface. The calculated thermal rate constant results were compared with reported values on the same surfaces. The success of these calculations demonstrates that time-independent vibrational configuration interaction can be a very convenient way to calculate converged quantum mechanical rate constants, and it opens the possibility of calculating converged rate constants for much larger reactions than have been treated until now.

Hot Temperature↗

Molecular clips form isostructural dimeric aggregates from benzene to water.

We report the synthesis and characterization of eight C-shaped methylene-bridged glycoluril dimers (1-8) bearing hydrogen-bonding amide groups on their aromatic rings. Compounds 1-6 undergo tight dimerization in CDCl3 solution (Ks > 9 x 10(5) M(-1)); binary mixtures of 1-7 form mixtures of homodimers and heterodimers in moderately selective dimerization processes (0.23 < or = Keq < or = 768; 0.253 < or = chiAB < 0.933). The high affinity formation of 1.1-6.6 is due to the commensurate nature of the geometrical constraints imposed by the pi-pi interactions and only two hydrogen bonds. The differential response of the strengths of the pi-pi interactions and H-bonds of 2.2 to changes in solvent polarity--from C6D6 to D2O--results in the formation of a solvent-independent isostructural aggregate that exhibits high affinity dimerization across the full range of solvents.

Benzene Derivatives↗

Calculation of converged rovibrational energies and partition function for methane using vibrational-rotational configuration interaction.

The rovibration partition function of CH4 was calculated in the temperature range of 100-1000 K using well-converged energy levels that were calculated by vibrational-rotational configuration interaction using the Watson Hamiltonian for total angular momenta J = 0-50 and the MULTIMODE computer program. The configuration state functions are products of ground-state occupied and virtual modals obtained using the vibrational self-consistent field method. The Gilbert and Jordan potential energy surface was used for the calculations. The resulting partition function was used to test the harmonic oscillator approximation and the separable-rotation approximation. The harmonic oscillator, rigid-rotator approximation is in error by a factor of 2.3 at 300 K, but we also propose a separable-rotation approximation that is accurate within 2% from 100 to 1000 K.

Journal Article↗

Methylene-bridged glycoluril dimers: synthetic methods.

Methylene-bridged glycoluril dimers are the fundamental building blocks of cucurbituril (CB[6]), its homologues (CB[n]), and its derivatives. This paper describes three complementary methods for the synthesis of C- and S-shaped methylene-bridged glycoluril dimers (29-34 and 37-44). For this purpose, we prepared glycoluril derivatives (1a-d) bearing diverse functionalities on their convex face. These glycoluril derivatives were alkylated under basic conditions (DMSO, t-BuOK) with 1,2-bis(halomethyl)aromatics 6-15 to yield 4a-d and 16-24, which contain a single aromatic o-xylylene ring and potentially nucleophilic ureidyl NH groups. Glycoluril derivatives bearing potentially electrophilic cyclic ether groups (5a-f) and 25-28 were prepared by various methods including condensation reactions in refluxing TFA containing paraformaldehyde. The condensation reactions of 4a-d and 16-24 with paraformaldehyde under anhydrous acidic conditions (PTSA, ClCH(2)CH(2)Cl, reflux) give, in most cases, the C-shaped and S-shaped methylene-bridged glycoluril in good to excellent yields. In many cases, the C-shaped compound is formed preferentially with high diastereoselectivity. Cyclic ethers 5a,d-f and 25-26 undergo highly diastereoselective dimerization reactions to yield methylene-bridged glycoluril dimers with the formal extrusion of formaldehyde. Last, it is possible to perform selective heterodimerization reactions using both cyclic ethers and glycoluril derivatives bearing ureidyl NH groups. These reactions deliver the desired C- and S-shaped heterodimers with low to moderate diastereoselectivities. This heterodimerization route is the method of choice in cases where the homodimerization reactions fail. The formation of side products (+/-)-35b and (+/-)-35d helps clarify the electronic requirements for a successful CB[n] synthesis. The X-ray structures of 30C, 38C, and 38S allow for a discussion of the structural features of this class of compounds.

Alkynes↗

Diastereoselective formation of glycoluril dimers: isomerization mechanism and implications for cucurbit[n]uril synthesis.

Cucurbit[6]uril (CB[6]) is a macrocyclic compound, prepared in one pot from glycoluril and formaldehyde, whose molecular recognition properties have made it the object of intense study. Studies of the mechanism of CB[n] formation, which might provide insights that allow the tailor-made synthesis of CB[n] homologues and derivatives, have been hampered by the complex structure of CB[n]. By reducing the complexity of the reaction to the formation of S-shaped (12S-18S) and C-shaped (12C-18C) methylene bridged glycoluril dimers, we have been able to probe the fundamental steps of the mechanism of CB[n] synthesis to a level that has not been possible previously. For example, we present strong evidence that the mechanism of CB[n] synthesis proceeds via the intermediacy of both S-shaped and C-shaped dimers. The first experimental determination of the relative free energies of the S-shaped and C-shaped dimers indicates a thermodynamic preference (1.55-3.25 kcal mol(-)(1)) for the C-shaped diastereomer. This thermodynamic preference is not because of self-association, solvation, or template effects. Furthermore, labeling experiments have allowed us to elucidate the mechanism of this acid-catalyzed equilibrium between the S-shaped and C-shaped diastereomers. The equilibration is an intramolecular process that proceeds with high diastereoselectivity and retention of configuration. On the basis of the broad implications of these results for CB[n] synthesis, we suggest new synthetic strategies that may allow for the improved preparation of CB[n] (n > 8) and CB[n] derivatives from functionalized glycolurils.

Alkynes↗