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Kim K. Baldridge

Bio: Kim K. Baldridge is an academic researcher from Tianjin University. The author has contributed to research in topics: Corannulene & Ab initio. The author has an hindex of 47, co-authored 248 publications receiving 25589 citations. Previous affiliations of Kim K. Baldridge include University of Zurich & Nankai University.


Papers
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Journal ArticleDOI
TL;DR: A description of the ab initio quantum chemistry package GAMESS, which can be treated with wave functions ranging from the simplest closed‐shell case up to a general MCSCF case, permitting calculations at the necessary level of sophistication.
Abstract: A description of the ab initio quantum chemistry package GAMESS is presented. Chemical systems containing atoms through radon can be treated with wave functions ranging from the simplest closed-shell case up to a general MCSCF case, permitting calculations at the necessary level of sophistication. Emphasis is given to novel features of the program. The parallelization strategy used in the RHF, ROHF, UHF, and GVB sections of the program is described, and detailed speecup results are given. Parallel calculations can be run on ordinary workstations as well as dedicated parallel machines. © John Wiley & Sons, Inc.

18,546 citations

Journal ArticleDOI
TL;DR: This assay suggests that conversion from green to red chromophores remains incomplete even after prolonged aging in DsRed, and quantitatively accounts for the red shift according to quantum mechanical calculations.
Abstract: DsRed, a brilliantly red fluorescent protein, was recently cloned from Discosoma coral by homology to the green fluorescent protein (GFP) from the jellyfish Aequorea. A core question in the biochemistry of DsRed is the mechanism by which the GFP-like 475-nm excitation and 500-nm emission maxima of immature DsRed are red-shifted to the 558-nm excitation and 583-nm emission maxima of mature DsRed. After digestion of mature DsRed with lysyl endopeptidase, high-resolution mass spectra of the purified chromophore-bearing peptide reveal that some of the molecules have lost 2 Da relative to the peptide analogously prepared from a mutant, K83R, that stays green. Tandem mass spectrometry indicates that the bond between the alpha-carbon and nitrogen of Gln-66 has been dehydrogenated in DsRed, extending the GFP chromophore by forming C==N==C==O at the 2-position of the imidazolidinone. This acylimine substituent quantitatively accounts for the red shift according to quantum mechanical calculations. Reversible hydration of the C==N bond in the acylimine would explain why denaturation shifts mature DsRed back to a GFP-like absorbance. The C==N bond hydrolyses upon boiling, explaining why DsRed shows two fragment bands on SDS/PAGE. This assay suggests that conversion from green to red chromophores remains incomplete even after prolonged aging.

617 citations

Journal ArticleDOI
TL;DR: In this paper, a detailed study of methods for generating the minimum energy path of a chemical reaction using ab initio electronic structure calculations is presented; the convergence with respect to step size of the geometry and energy along this path is studied with several algorithms.
Abstract: A detailed study of methods for generating the minimum energy path of a chemical reaction using ab initio electronic structure calculations is presented; the convergence with respect to step size of the geometry and energy along this path is studied with several algorithms. The investigations are extended to the calculation of chemical reaction rate coefficients by interfacing the polyrate code for variational transition-state theory and semiclassical tunneling calculations with a locally modified Gaussian 82 electronic structure package that now contains reaction path following capabilities at both the Hartree-Fock and perturbation theory levels. This combined package is used to study the kinetics of the abstraction reaction CH{sub 3} + H{sub 2} {yields} CH{sub 4} + H, which is considered as a prototype organic reaction. They report calculations of reaction rates based on electronic structure theory and generalized transition-state theory, including a multidimensional tunneling correction, without performing an analytic fit to the potential surface. The calculation of dynamical processes directly from ab initio electronic structure input without the intermediary of a potential surface fit is called direct dynamics, and this paper demonstrates the feasibility of this approach for bimolecular reactions.

329 citations

Journal ArticleDOI
TL;DR: Synthesis of a series of corannulene derivatives with varying bowl depths has allowed for a study correlating the structure (bowl depth) and the energy of bowl inversion.
Abstract: Synthesis of a series of corannulene derivatives with varying bowl depths has allowed for a study correlating the structure (bowl depth) and the energy of bowl inversion. Substituents placed in the peri positions are repulsive and flatten the bowl, thus causing a decrease in the bowl inversion barrier. Conversely, annelation across the peri positions causes a deepening of the bowl, thus an increase in the bowl inversion barrier. Barriers between 8.7 and 17.3 kcal/mol have been measured, and their structures have been calculated using a variety of ab initio methods. The energy profile of an individual corannulene derivative is assumed to fit a mixed quartic/quadratic function from which an empirical correlation of bowl depth and inversion barrier that follows a quartic function is derived. Structure/energy correlations of this type speak broadly of the nature of enzymatic and catalytic activation of substrates.

236 citations

Journal ArticleDOI
29 Apr 2011-Science
TL;DR: It is shown that phenyl cation equivalents, generated from otherwise unreactive aryl fluorides, allow extension of the Friedel-Crafts reaction to intramolecular aries couplings, and Silicon-fluorine bond formation expands the range of compounds that can be used in a reaction that forms carbon-carbon bonds.
Abstract: The venerable Friedel-Crafts reaction appends alkyl or acyl groups to aromatic rings through alkyl or acyl cation equivalents typically generated by Lewis acids. We show that phenyl cation equivalents, generated from otherwise unreactive aryl fluorides, allow extension of the Friedel-Crafts reaction to intramolecular aryl couplings. The enabling feature of this reaction is the exchange of carbon-fluorine for silicon-fluorine bond enthalpies; the reaction is activated by an intermediate silyl cation. Catalytic quantities of protons or silyl cations paired with weakly coordinating carborane counterions initiate the reactions, after which proton transfer in the final aromatization step regenerates the active silyl cation species by protodesilylation of a quaternary silane. The methodology allows the high-yield formation of a range of tailored polycyclic aromatic hydrocarbons and graphene fragments.

236 citations


Cited by
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Journal ArticleDOI
TL;DR: QUANTUM ESPRESSO as discussed by the authors is an integrated suite of computer codes for electronic-structure calculations and materials modeling, based on density functional theory, plane waves, and pseudopotentials (norm-conserving, ultrasoft, and projector-augmented wave).
Abstract: QUANTUM ESPRESSO is an integrated suite of computer codes for electronic-structure calculations and materials modeling, based on density-functional theory, plane waves, and pseudopotentials (norm-conserving, ultrasoft, and projector-augmented wave). The acronym ESPRESSO stands for opEn Source Package for Research in Electronic Structure, Simulation, and Optimization. It is freely available to researchers around the world under the terms of the GNU General Public License. QUANTUM ESPRESSO builds upon newly-restructured electronic-structure codes that have been developed and tested by some of the original authors of novel electronic-structure algorithms and applied in the last twenty years by some of the leading materials modeling groups worldwide. Innovation and efficiency are still its main focus, with special attention paid to massively parallel architectures, and a great effort being devoted to user friendliness. QUANTUM ESPRESSO is evolving towards a distribution of independent and interoperable codes in the spirit of an open-source project, where researchers active in the field of electronic-structure calculations are encouraged to participate in the project by contributing their own codes or by implementing their own ideas into existing codes.

19,985 citations

28 Jul 2005
TL;DR: PfPMP1)与感染红细胞、树突状组胞以及胎盘的单个或多个受体作用,在黏附及免疫逃避中起关键的作�ly.
Abstract: 抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1(PfPMP1)与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用,在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员,通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

18,940 citations

Journal ArticleDOI
TL;DR: A description of the ab initio quantum chemistry package GAMESS, which can be treated with wave functions ranging from the simplest closed‐shell case up to a general MCSCF case, permitting calculations at the necessary level of sophistication.
Abstract: A description of the ab initio quantum chemistry package GAMESS is presented. Chemical systems containing atoms through radon can be treated with wave functions ranging from the simplest closed-shell case up to a general MCSCF case, permitting calculations at the necessary level of sophistication. Emphasis is given to novel features of the program. The parallelization strategy used in the RHF, ROHF, UHF, and GVB sections of the program is described, and detailed speecup results are given. Parallel calculations can be run on ordinary workstations as well as dedicated parallel machines. © John Wiley & Sons, Inc.

18,546 citations

Journal ArticleDOI
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

Journal ArticleDOI
TL;DR: This paper presents a meta-modelling procedure called "Continuum Methods within MD and MC Simulations 3072", which automates the very labor-intensive and therefore time-heavy and expensive process of integrating discrete and continuous components into a discrete-time model.
Abstract: 6.2.2. Definition of Effective Properties 3064 6.3. Response Properties to Magnetic Fields 3066 6.3.1. Nuclear Shielding 3066 6.3.2. Indirect Spin−Spin Coupling 3067 6.3.3. EPR Parameters 3068 6.4. Properties of Chiral Systems 3069 6.4.1. Electronic Circular Dichroism (ECD) 3069 6.4.2. Optical Rotation (OR) 3069 6.4.3. VCD and VROA 3070 7. Continuum and Discrete Models 3071 7.1. Continuum Methods within MD and MC Simulations 3072

13,286 citations