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Cyanuric acid (CA), a triazine heterocycle, is extensively utilized for noncovalent self‐assembly. The association between poly(adenine) and CA into micron‐length fibers was a remarkable observation made by Sleiman and co‐workers, who proposed that adenine and CA adopt a hexameric rosette configuration in analogy with previously reported structures for CA assemblies. However, recent experimental observations from the Krishnamurthy group led to a reevaluation of the hexameric rosette model, wherein they have proposed a hydrogen‐bonded helicene model as an alternative. Our molecular dynamics simulations show that the hexad model is indeed unlikely and that this novel noncovalent helicene geometry, where the adenine and CA bases form an extended helical hydrogen‐bond network across the system, is a more probable structural motif. The existence of noncovalent helicene compounds may have wide‐ranging applications in DNA nanotechnology and helicene chemistry. [ABSTRACT FROM AUTHOR]

The study of noncovalent interactions, notably including drug-protein binding, relies heavily on the language of localized functional group contacts: hydrogen bonding, π-π interactions, CH-π contacts, halogen bonding, etc. Applying the state-of-the-art functional group symmetry-adapted perturbation theory (F-SAPT) to an important question of chloro versus methyl aryl substitution in factor Xa inhibitor drugs, we find that a localized contact model provides an incorrect picture for the origin of the enhancement of chloro-containing ligands. Instead, the enhancement is found to originate from many intermediate-range contacts distributed throughout the binding pocket, particularly including the peptide bonds in the protein backbone. The contributions from these contacts are primarily electrostatic in nature, but require ab initio computations involving nearly the full drug-protein pocket system to be accurately quantified. [ABSTRACT FROM AUTHOR]

The structural and electronic consequences of π-π and C-H/π interactions in two alkoxy-substituted 1,8-bis-((propyloxyphenyl)ethynyl)naphthalenes are explored by using X-ray crystallography and electronic structure compu tations. The crystal structure of analogue 4, bearing an alkoxy side chain in the 4-position of each of the phenyl rings, adopts a π-stacked geometry, whereas analogue 8, bearing alkoxy groups at both the 2- and the 5-positions of each ring, has a geometry in which the rings are splayed away from a π-stacked arrangement. Symmetry-adapted per turbation theory analysis was performed on the two ana logues to evaluate the interactions between the phenyle-thynyl arms in each molecule in terms of electrostatic, steric, polarization, and London dispersion components. The computations support the expectation that the π-stacked geometry of the alkoxyphenyl units in 4 is simply a consequence of maximizing P-P interactions. However, the splayed geometry of 8 results from a more subtle competition between different noncovalent interactions: this geometry provides a favorable anti-alignment of C-O bond dipoles, and two C-H/π interactions in which hydrogen atoms of the alkyl side chains interact favorably with the π electrons of the other phenyl ring. These favorable interactions overcome competing π-π interactions to give rise to a geometry in which the phenylethynyl substituents are in an offset, un-stacked arrangement. [ABSTRACT FROM AUTHOR]

The Psi4 program is a new approach to modern quantum chemistry, encompassing Hartree-Fock and density-functional theory to configuration interaction and coupled cluster. The program is written entirely in C++ and relies on a new infrastructure that has been designed to permit high-efficiency computations of both standard and emerging electronic structure methods on conventional and high-performance parallel computer architectures. Psi4 offers flexible user input built on the Python scripting language that enables both new and experienced users to make full use of the program's capabilities, and even to implement new functionality with moderate effort. To maximize its impact and usefulness, Psi4 is available through an open-source license to the entire scientific community. © 2011 John Wiley & Sons, Ltd. [ABSTRACT FROM AUTHOR]

Noncovalent interactions remain poorly understood despite their importance to supramolecular chemistry, biochemistry, and materials science. They are an ideal target for theoretical study, where interactions of interest can be probed directly, free from competing secondary interactions. However, the most popular tools of computational chemistry are not particularly reliable for noncovalent interactions. Here we review recent works in wavefunction-based quantum chemistry techniques aimed at greater accuracy and faster computations for these systems. We describe recent developments in high-accuracy benchmarks, a variety of recent wavefunction methods with promise for noncovalent interactions, various approximations to speed up these methods, and recent advances in wavefunction-based symmetry-adapted perturbation theory, which provides not only interaction energies but also their decomposition into physically meaningful components. Together, these advances are currently extending robust, accurate computations of noncovalent interactions from systems with around one dozen heavy atoms up to systems with several dozens of heavy atoms. © 2011 John Wiley & Sons, Ltd. [ABSTRACT FROM AUTHOR]

Several popular force fields, namely, CHARMM, AMBER, OPLS-AA, and MM3, have been tested for their ability to reproduce highly accurate quantum mechanical potential energy curves for noncovalent interactions in the benzene dimer, the benzene-CH4 complex, and the benzene-H2S complex. All of the force fields are semi-quantitatively correct, but none of them is consistently reliable quantitatively. Re-optimization of Lennard-Jones parameters and symmetry-adapted perturbation theory analysis for the benzene dimer suggests that better agreement cannot be expected unless more flexible functional forms (particularly for the electrostatic contributions) are employed for the empirical force fields. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009 [ABSTRACT FROM AUTHOR]

Recent photofragment fluorescence excitation (PHOFEX) spectroscopy experiments have observed the Ã1A″ singlet excited state of isocyanogen (CNCN) for the first time. The observed spectrum is not completely assigned and significant questions remain about the excited states of this system. To provide insight into the energetically accessible excited states of CNCN, optimized geometries, harmonic vibrational frequencies, and excitation energies for the first three singlet excited states are determined using equation-of-motion coupled-cluster theory with singles and doubles (EOM-CCSD) and correlation-consistent basis sets. Additionally, excited state coupled-cluster methods which approximate the contributions from triples (CC3) are utilized to estimate the effect of higher-order correlation on the energy of each excited state. For the Ã1A″ state, our best estimate for T0 is about 42,200 cm-1, in agreement with the experimentally estimated upper limit for the zero-point level of 42,523 cm-1. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008 [ABSTRACT FROM AUTHOR]

S/π interactions are prevalent in biochemistry and play an important role in protein folding and stabilization. Geometries of cysteine/aromatic interactions found in crystal structures from the Brookhaven Protein Data Bank (PDB) are analyzed and compared with the equilibrium configurations predicted by high-level quantum mechanical results for the H2S-benzene complex. A correlation is observed between the energetically favorable configurations on the quantum mechanical potential energy surface of the H2S-benzene model and the cysteine/aromatic configurations most frequently found in crystal structures of the PDB. In contrast to some previous PDB analyses, configurations with the sulfur over the aromatic ring are found to be the most important. Our results suggest that accurate quantum computations on models of noncovalent interactions may be helpful in understanding the structures of proteins and other complex systems. [ABSTRACT FROM AUTHOR]

PSI3 is a program system and development platform for ab initio molecular electronic structure computations. The package includes mature programming interfaces for parsing user input, accessing commonly used data such as basis-set information or molecular orbital coefficients, and retrieving and storing binary data (with no software limitations on file sizes or file-system-sizes), especially multi-index quantities such as electron repulsion integrals. This platform is useful for the rapid implementation of both standard quantum chemical methods, as well as the development of new models. Features that have already been implemented include Hartree-Fock, multiconfigurational self-consistent-field, second-order Møller-Plesset perturbation theory, coupled cluster, and configuration interaction wave functions. Distinctive capabilities include the ability to employ Gaussian basis functions with arbitrary angular momentum levels; linear R12 second-order perturbation theory; coupled cluster frequency-dependent response properties, including dipole polarizabilities and optical rotation; and diagonal Born-Oppenheimer corrections with correlated wave functions. This article describes the programming infrastructure and main features of the package. PSI3 is available free of charge through the open-source, GNU General Public License. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007 [ABSTRACT FROM AUTHOR]

The restrained electrostatic potential (RESP) charge model is widely used in molecular dynamics simulations, especially for the AMBER and GAFF force fields. We have implemented the RESP scheme using the accessible and widely used Python language and the NumPy numerical library. This article provides a programming‐oriented introduction to the RESP scheme and highlights some of the features of NumPy that are useful in scientific computing. [ABSTRACT FROM AUTHOR]