Author
Shahar Keinan
Other affiliations: Polaris Industries, University of North Carolina at Chapel Hill, Durham University ...read more
Bio: Shahar Keinan is an academic researcher from Research Triangle Park. The author has contributed to research in topics: Targeted drug delivery & Prodrug. The author has an hindex of 24, co-authored 54 publications receiving 7414 citations. Previous affiliations of Shahar Keinan include Polaris Industries & University of North Carolina at Chapel Hill.
Papers published on a yearly basis
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TL;DR: This work develops an approach to detect noncovalent interactions in real space, based on the electron density and its derivatives, which provides a rich representation of van der Waals interactions, hydrogen bonds, and steric repulsion in small molecules, molecular complexes, and solids.
Abstract: Molecular structure does not easily identify the intricate noncovalent interactions that govern many areas of biology and chemistry, including design of new materials and drugs. We develop an approach to detect noncovalent interactions in real space, based on the electron density and its derivatives. Our approach reveals the underlying chemistry that compliments the covalent structure. It provides a rich representation of van der Waals interactions, hydrogen bonds, and steric repulsion in small molecules, molecular complexes, and solids. Most importantly, the method, requiring only knowledge of the atomic coordinates, is efficient and applicable to large systems, such as proteins or DNA. Across these applications, a view of nonbonded interactions emerges as continuous surfaces rather than close contacts between atom pairs, offering rich insight into the design of new and improved ligands.
5,731 citations
TL;DR: The NCI computational algorithms and their implementation for the analysis and visualization of weak interactions, using both self-consistent fully quantum-mechanical, as well as promolecular, densities are described.
Abstract: Noncovalent interactions hold the key to understanding many chemical, biological, and technological problems. Describing these noncovalent interactions accurately, including their positions in real space, constitutes a first step in the process of decoupling the complex balance of forces that define noncovalent interactions. Because of the size of macromolecules, the most common approach has been to assign van der Waals interactions (vdW), steric clashes (SC), and hydrogen bonds (HBs) based on pairwise distances between atoms according to their vdW radii. We recently developed an alternative perspective, derived from the electronic density: the non-covalent interactions (NCI) index [J. Am. Chem. Soc. 2010, 132, 6498]. This index has the dual advantages of being generally transferable to diverse chemical applications and being very fast to compute, since it can be calculated from promolecular densities. Thus, NCI analysis is applicable to large systems, including proteins and DNA, where analysis of noncova...
2,596 citations
TL;DR: Recent studies are described that address puzzling questions of how conformational distributions, excited-state polarization, and electronic and nuclear dynamical effects influence ET in macromolecules, including the tunneling, resonant transport, and hopping regimes.
Abstract: Electron transfer (ET) reactions provide a nexus among chemistry, biochemistry, and physics. These reactions underpin the “power plants” and “power grids” of bioenergetics, and they challenge us to understand how evolution manipulates structure to control ET kinetics. Ball-and-stick models for the machinery of electron transfer, however, fail to capture the rich electronic and nuclear dynamics of ET molecules: these static representations disguise, for example, the range of thermally accessible molecular conformations. The influence of structural fluctuations on electron-transfer kinetics is amplified by the exponential decay of electron tunneling probabilities with distance, as well as the delicate interference among coupling pathways. Fluctuations in the surrounding medium can also switch transport between coherent and incoherent ET mechanisms − and may gate ET so that its kinetics is limited by conformational interconversion times, rather than by the intrinsic ET time scale. Moreover, preparation of a ...
155 citations
TL;DR: It is concluded that both thermal hopping and superexchange should contribute significantly to charge transfer even in short DNA/PNA fragments, and PNA is found to be more flexible than DNA, and this flexibility is predicted to produce larger rates of charge transfer.
Abstract: The effects of structural fluctuations on charge transfer in double-stranded DNA and peptide nucleic acid (PNA) are investigated. A palindromic sequence with two guanine bases that play the roles of hole donor and acceptor, separated by a bridge of two adenine bases, was analyzed using combined molecular dynamics (MD) and quantum-chemical methods. Surprisingly, electronic structure calculations on individual MD snapshots show significant frontier orbital electronic population on the bridge in ∼10% of the structures. Electron-density delocalization to the bridge is found to be gated by fluctuations of the covalent conjugated bond structure of the aromatic rings of the nucleic bases. It is concluded, therefore, that both thermal hopping and superexchange should contribute significantly to charge transfer even in short DNA/PNA fragments. PNA is found to be more flexible than DNA, and this flexibility is predicted to produce larger rates of charge transfer.
110 citations
TL;DR: An emerging framework is described for understanding the diversity of charge transport mechanisms seen in nucleic acids through the influences of nucleobase geometry, electronic structure, solvent environment, and thermal conformational fluctuations.
108 citations
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TL;DR: Five practical examples involving a wide variety of systems and analysis methods are given to illustrate the usefulness of Multiwfn, a multifunctional program for wavefunction analysis.
Abstract: Multiwfn is a multifunctional program for wavefunction analysis. Its main functions are: (1) Calculating and visualizing real space function, such as electrostatic potential and electron localization function at point, in a line, in a plane or in a spatial scope. (2) Population analysis. (3) Bond order analysis. (4) Orbital composition analysis. (5) Plot density-of-states and spectrum. (6) Topology analysis for electron density. Some other useful utilities involved in quantum chemistry studies are also provided. The built-in graph module enables the results of wavefunction analysis to be plotted directly or exported to high-quality graphic file. The program interface is very user-friendly and suitable for both research and teaching purpose. The code of Multiwfn is substantially optimized and parallelized. Its efficiency is demonstrated to be significantly higher than related programs with the same functions. Five practical examples involving a wide variety of systems and analysis methods are given to illustrate the usefulness of Multiwfn. The program is free of charge and open-source. Its precompiled file and source codes are available from http://multiwfn.codeplex.com.
17,273 citations
TL;DR: This work develops an approach to detect noncovalent interactions in real space, based on the electron density and its derivatives, which provides a rich representation of van der Waals interactions, hydrogen bonds, and steric repulsion in small molecules, molecular complexes, and solids.
Abstract: Molecular structure does not easily identify the intricate noncovalent interactions that govern many areas of biology and chemistry, including design of new materials and drugs. We develop an approach to detect noncovalent interactions in real space, based on the electron density and its derivatives. Our approach reveals the underlying chemistry that compliments the covalent structure. It provides a rich representation of van der Waals interactions, hydrogen bonds, and steric repulsion in small molecules, molecular complexes, and solids. Most importantly, the method, requiring only knowledge of the atomic coordinates, is efficient and applicable to large systems, such as proteins or DNA. Across these applications, a view of nonbonded interactions emerges as continuous surfaces rather than close contacts between atom pairs, offering rich insight into the design of new and improved ligands.
5,731 citations
TL;DR: The NCI computational algorithms and their implementation for the analysis and visualization of weak interactions, using both self-consistent fully quantum-mechanical, as well as promolecular, densities are described.
Abstract: Noncovalent interactions hold the key to understanding many chemical, biological, and technological problems. Describing these noncovalent interactions accurately, including their positions in real space, constitutes a first step in the process of decoupling the complex balance of forces that define noncovalent interactions. Because of the size of macromolecules, the most common approach has been to assign van der Waals interactions (vdW), steric clashes (SC), and hydrogen bonds (HBs) based on pairwise distances between atoms according to their vdW radii. We recently developed an alternative perspective, derived from the electronic density: the non-covalent interactions (NCI) index [J. Am. Chem. Soc. 2010, 132, 6498]. This index has the dual advantages of being generally transferable to diverse chemical applications and being very fast to compute, since it can be calculated from promolecular densities. Thus, NCI analysis is applicable to large systems, including proteins and DNA, where analysis of noncova...
2,596 citations
TL;DR: A new geometric parameter for four-coordinate compounds, tau(4), is proposed as an improved, simple metric for quantitatively evaluating the geometry of four- coordinate complexes and compounds.
Abstract: Four Cu(I) complexes were synthesized with a family of pyridylmethylamide ligands, HLR [HLR = N-(2-pyridylmethyl)acetamide, R = null; 2,2-dimethyl-N-(2-pyridylmethyl)propionamide, R = Me3; 2,2,2-triphenyl-N-(2-pyridylmethyl)acetamide, R = Ph3)]. Complexes 1–3 were synthesized from the respective ligand and [Cu(CH3CN)4]PF6 in a 2 : 1 molar ratio: [Cu(HL)2]PF6 (1), [Cu2(HLMe3)4](PF6)2 (2), [Cu(HLPh3)2]PF6 (3). Complex 4, [Cu(HL)(CH3CN)(PPh3)]PF6, was synthesized from the reaction of HL with [Cu(CH3CN)4]PF6 and PPh3 in a 1 : 1 : 1 molar ratio. X-Ray crystal structures reveal that complexes 1, 3 and 4 are mononuclear Cu(I) species, while complex 2 is a Cu(I) dimer. The copper ions are four-coordinate with geometries ranging from distorted tetrahedral to seesaw in 1, 2, and 4. Complexes 1 and 2 are very air sensitive and they display similar electrochemical properties. The coordination geometry of complex 3 is nearly linear, two-coordinate. Complex 3 is exceptionally stable with respect to oxidation in the air, and its cyclic voltammetry shows no oxidation wave in the range of 0–1.5 V. The unusual inertness of complex 3 towards oxidation is attributed to the protection from bulky triphenyl substituent of the HLPh3 ligand. A new geometric parameter for four-coordinate compounds, τ4, is proposed as an improved, simple metric for quantitatively evaluating the geometry of four-coordinate complexes and compounds.
2,281 citations
TL;DR: Jaguar as mentioned in this paper is an ab initio quantum chemical program that specializes in fast electronic structure predictions for molecular systems of medium and large size, such as density functional theory (DFT) and local second-order Moller-Plesset perturbation theory.
Abstract: Jaguar is an ab initio quantum chemical program that specializes in fast electronic structure predictions for molecular systems of medium and large size. Jaguar focuses on computational methods with reasonable computational scaling with the size of the system, such as density functional theory (DFT) and local second-order Moller–Plesset perturbation theory. The favorable scaling of the methods and the high efficiency of the program make it possible to conduct routine computations involving several thousand molecular orbitals. This performance is achieved through a utilization of the pseudospectral approximation and several levels of parallelization. The speed advantages are beneficial for applying Jaguar in biomolecular computational modeling. Additionally, owing to its superior wave function guess for transition-metal-containing systems, Jaguar finds applications in inorganic and bioinorganic chemistry. The emphasis on larger systems and transition metal elements paves the way toward developing Jaguar for its use in materials science modeling. The article describes the historical and new features of Jaguar, such as improved parallelization of many modules, innovations in ab initio pKa prediction, and new semiempirical corrections for nondynamic correlation errors in DFT. Jaguar applications in drug discovery, materials science, force field parameterization, and other areas of computational research are reviewed. Timing benchmarks and other results obtained from the most recent Jaguar code are provided. The article concludes with a discussion of challenges and directions for future development of the program. © 2013 Wiley Periodicals, Inc.
1,307 citations