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PubMed2003

Computation of multicenter overlap integrals with Slater-type orbitals using psi(alpha)-ETOs.

Multicenter overlap integrals appearing in the evaluation of multicenter-multielectron integrals of central and noncentral interaction potentials are calculated using complete orthonormal sets of psi(alpha)-ETOs (alpha=1, 0, -1, -2,...). The final results are expressed in terms of two-center overlap integrals between STOs. The convergence of the series is tested by calculating concrete cases for arbitrary quantum numbers, screening constants and location of STOs.

Computers↗

PubMed1996

Novel methods for molecular dynamics simulations.

In the past year, significant progress was made in the development of molecular dynamics methods for the liquid phase and for biological macromolecules. Specifically, faster algorithms to pursue molecular dynamics simulations were introduced and advances were made in the design of new optimization algorithms guided by molecular dynamics protocols. A technique to calculate the quantum spectra of protein vibrations was introduced.

Algorithms↗

PubMed2006

Contributions of long-range electrostatic interactions to 4-chlorobenzoyl-CoA dehalogenase catalysis: a combined theoretical and experimental study.

It is well established that electrostatic interactions play a vital role in enzyme catalysis. In this work, we report theory-guided mutation experiments that identified strong electrostatic contributions of a remote residue, namely, Glu232 located on the adjacent subunit, to 4-chlorobenzoyl-CoA dehalogenase catalysis. The Glu232Asp mutant was found to bind the substrate analogue 4-methylbenzoyl-CoA more tightly than does the wild-type dehalogenase. In contrast, the kcat for 4-chlorobenzoyl-CoA conversion to product was reduced 10000-fold in the mutant. UV difference spectra measured for the respective enzyme-ligand complexes revealed an approximately 3-fold shift in the equilibrium of the two active site conformers away from that inducing strong pi-electron polarization in the ligand benzoyl ring. Increased substrate binding, decreased ring polarization, and decreased catalytic efficiency indicated that the repositioning of the point charge in the Glu232Asp mutant might affect the orientation of the Asp145 carboxylate with respect to the substrate aromatic ring. The time course for formation and reaction of the arylated enzyme intermediate during a single turnover was measured for wild-type and Glu232Asp mutant dehalogenases. The accumulation of arylated enzyme in the wild-type dehalogenase was not observed in the mutant. This indicates that the reduced turnover rate in the mutant is the result of a slow arylation of Asp145, owing to decreased efficiency in substrate nucleophilic attack by Asp145. To rationalize the experimental observations, a theoretical model is proposed, which computes the potential of mean force for the nucleophilic aromatic substitution step using a hybrid quantum mechanical/molecular mechanical method. To this end, the removal or reorientation of the side chain charge of residue 232, modeled respectively by the Glu232Gln and Glu232Asp mutants, is shown to increase the rate-limiting energy barrier. The calculated 23.1 kcal/mol free energy barrier for formation of the Meisenheimer intermediate in the Glu232Asp mutant represents an increase of 6 kcal/mol relative to that of the wild-type enzyme, consistent with the 5.6 kcal/mol increase calculated from the difference in experimentally determined rate constants. On the basis of the combination of the experimental and theoretical evidence, we hypothesize that the Glu232(B) residue contributes to catalysis by providing an electrostatic force that acts on the Asp145 nucleophile.

Amino Acid Substitution↗

PubMed2006

Solid-state 35/37Cl NMR spectroscopy of hydrochloride salts of amino acids implicated in chloride ion transport channel selectivity: opportunities at 900 MHz.

The results of a detailed systematic chlorine solid-state NMR study of several hydrochloride salts of amino acids implicated in chloride ion transport channel selectivity are reported. (35)Cl and (37)Cl NMR spectra have been obtained for stationary and/or magic-angle spinning powdered samples of the following compounds on 500 and/or 900 MHz spectrometers: DL-arginine HCl monohydrate, L-lysine HCl, L-serine HCl, L-glutamic acid HCl, L-proline HCl, L-isoleucine HCl, L-valine HCl, L-phenylalanine HCl, and glycine HCl. Spectral analyses provide information on the anisotropic properties and relative orientations of the chlorine electric field gradient and chemical shift (CS) tensors, which are intimately related to the local molecular and electronic structure. Data obtained at 900 MHz provide unique examples of the effects of CS anisotropy on the NMR spectrum of a quadrupolar nucleus. The range of chlorine quadrupolar coupling constants (C(Q)) measured, -6.42 to 2.03 MHz, demonstrates the sensitivity of this parameter to the chloride ion environment and suggests the applicability of chlorine solid-state NMR as a novel experimental tool for defining chloride binding environments in larger ion channel systems. Salts of hydrophobic amino acids are observed to tend to exhibit larger values of C(Q) than salts of hydrophilic amino acids. A simple model for rationalizing the observed trend in C(Q) is proposed. For salts for which neutron diffraction structures are available, we identify a quantum chemical method which reproduces experimental values of C(Q) with a root-mean-square deviation of 0.1 MHz and a correlation coefficient of 0.9998. On the basis of this, chlorine NMR tensors are predicted for the Cl(-) binding site in ClC channels.

Amino Acids↗

PubMed2006

On the electronic origin of strain energy: QTAIM study of perfluorocycloalkanes.

The strain energies (SE) of the five smallest perfluorocycloalkanes (c-CnF2n; n=3, 4, 5, 6, and 7) were calculated by means of several homodesmotic processes using B3LYP/6-31++G(d,p) optimized molecular energies. These values were compared with the energy difference between the linear and cyclic CF2 groups calculated by means of the quantum theory of atoms in molecules (QTAIM) applied on charge densities obtained at the same computational level. The differences between the values computed with both methods vary from 255 (n=3) to 629 (n=7) kJ mol-1. These differences arise because QTAIM-computed SE contain the energy involved in opening the ring to give rise to nearly transferable central CF2 fragments of linear perfluoroalkanes, whereas homodesmotic energies contain energy terms corresponding to transformation of nontransferable linear CF2 fragments and a ring-opening energy, which depending on the process, transforms CF2 cyclic compounds into nearly transferable or nontransferable linear CF2 groups.

Journal Article↗

PubMed2004

Second-order Møller-Plesset theory with linear R12 terms (MP2-R12) revisited: auxiliary basis set method and massively parallel implementation.

Ab initio electronic structure approaches in which electron correlation explicitly appears have been the subject of much recent interest. Because these methods accelerate the rate of convergence of the energy and properties with respect to the size of the one-particle basis set, they promise to make accuracies of better than 1 kcal/mol computationally feasible for larger chemical systems than can be treated at present with such accuracy. The linear R12 methods of Kutzelnigg and co-workers are currently the most practical means to include explicit electron correlation. However, the application of such methods to systems of chemical interest faces severe challenges, most importantly, the still steep computational cost of such methods. Here we describe an implementation of the second-order Møller-Plesset method with terms linear in the interelectronic distances (MP2-R12) which has a reduced computational cost due to the use of two basis sets. The use of two basis sets in MP2-R12 theory was first investigated recently by Klopper and Samson and is known as the auxiliary basis set (ABS) approach. One of the basis sets is used to describe the orbitals and another, the auxiliary basis set, is used for approximating matrix elements occurring in the exact MP2-R12 theory. We further extend the applicability of the approach by parallelizing all steps of the integral-direct MP2-R12 energy algorithm. We discuss several variants of the MP2-R12 method in the context of parallel execution and demonstrate that our implementation runs efficiently on a variety of distributed memory machines. Results of preliminary applications indicate that the two-basis (ABS) MP2-R12 approach cannot be used safely when small basis sets (such as augmented double- and triple-zeta correlation consistent basis sets) are utilized in the orbital expansion. Our results suggest that basis set reoptimization or further modifications of the explicitly correlated ansatz and/or standard approximations for matrix elements are necessary in order to make the MP2-R12 method sufficiently accurate when small orbital basis sets are used. The computer code is a part of the latest public release of Sandia's Massively Parallel Quantum Chemistry program available under GNU General Public License.

Journal Article↗

PubMed2005

Applications of a time correlation function theory for the fifth-order Raman response function I: atomic liquids.

Multidimensional spectroscopy has the ability to provide great insight into the complex dynamics and time-resolved structure of liquids. Theoretically describing these experiments requires calculating the nonlinear-response function, which is a combination of quantum-mechanical time correlation functions R5(t1,t2) was expressed with a two-time, computationally tractable, classical TCF. Writing the response function in terms of classical TCFs brings the full power of atomistically detailed molecular dynamics to the problem. In this paper, the new TCF theory is employed to calculate the fifth-order Raman response function for liquid xenon and investigate several of the polarization conditions for which experiments can be performed on an isotropic system. The theory is shown to reproduce line-shape characteristics predicted by earlier theoretical work.

Journal Article↗

PubMed2004

Neuromagnetic field strength outside the human head due to impedance changes from neuronal depolarization.

The holy grail of neuroimaging would be to have an imaging system, which could image neuronal electrical activity over milliseconds. One way to do this would be by imaging the impedance changes associated with ion channels opening in neuronal membranes in the brain during activity. In principle, we could measure this change by using electrical impedance tomography (EIT) but it is close to its threshold of detectability. With the inherent limitation in the use of electrodes, we propose a new scheme based on recording the magnetic field resulting from an injected current with superconducting quantum interference devices (SQUIDs), used in magnetoencephalography (MEG). We have performed a feasibility study using computer simulation. The head was modelled as concentric spheres to mimic the scalp, skull, cerebrospinal fluid and brain using the finite element method. The magnetic field 1 cm away from the scalp was estimated. An impedance change of 1% in a 2 cm radius volume in the brain was modelled as the region of depolarization. A constant current of 100 microA was injected into the head from diametrically opposite electrodes. The model predicts that the standing magnetic field is about 10 pT and changed by about 3 fT (0.03%) on depolarization. The spectral noise density in a typical MEG system in the frequency band 1-100 Hz is about 7 fT, so this places the change at the limit of detectability. This is similar to electrical recording, as in conventional EIT systems, but there may be advantages to MEG in that the magnetic field directly traverses the skull and instrumentation errors from the electrode-skin interface will be obviated.

Electric Impedance↗

PubMed1999

Spectrum of stochastic evolution operators: local matrix representation approach.

A matrix representation of the evolution operator associated with a nonlinear stochastic flow with additive noise is used to compute its spectrum. In the weak noise limit a perturbative expansion for the spectrum is formulated in terms of local matrix representations of the evolution operator centered on classical periodic orbits. The evaluation of perturbative corrections is easier to implement in this framework than in the standard Feynman diagram perturbation theory. The results are perturbative corrections to a stochastic analog of the Gutzwiller semiclassical spectral determinant computed to several orders beyond what has so far been attainable in stochastic and quantum-mechanical applications.

Journal Article↗

PubMed2005

Test of a numerical approach to the quantization of billiards.

A method for computing large numbers of eigenvalues of self-adjoint elliptic operators [J. Comput. Phys. 184, 321 (2003)] is tested in numerical studies of the spectral properties of quantum billiards. To this extent, we study a time-reversal invariant quantum billiard of threefold symmetry, that undergoes a transformation in its symmetry properties from C(3v) to C3 . Thereby a transition from Gaussian orthogonal to Gaussian unitary ensemble statistics is observed, verifying earlier experimental indications and theoretical predictions. At the same time our numerical ansatz is shown to be applicable to arbitrary billiard shapes.

Journal Article↗

PubMed2000

Mobile bipolaron

We explore the properties of the bipolaron in a 1D Holstein-Hubbard model with dynamical quantum phonons. Using a recently developed variational method combined with analytical strong coupling calculations, we compute correlation functions, effective mass, bipolaron isotope effect, and the phase diagram. The two site bipolaron has a significantly reduced mass and isotope effect compared to the on-site bipolaron, and is bound in the strong coupling regime up to twice the Hubbard U naively expected. The model can be described in this regime as an effective t-J-V model with nearest neighbor repulsion. These are the most accurate bipolaron calculations to date.

Journal Article↗

PubMed2006

Scarring by homoclinic and heteroclinic orbits.

In addition to the well-known scarring effect of periodic orbits, we show here that homoclinic and heteroclinic orbits, which are cornerstones in the theory of classical chaos, also scar eigenfunctions of classically chaotic systems when associated closed circuits in phase space are properly quantized, thus introducing strong quantum correlations. The corresponding quantization rules are also established. This opens the door for developing computationally tractable methods to calculate eigenstates of chaotic systems.

Journal Article↗

PubMed1999

Density functional theory of biologically relevant metal centers.

Recent applications of density functional theory to biologically relevant metal centers are reviewed. The emphasis is on reaction mechanisms, structures, and modeling. The accuracy of different functionals is discussed for standard benchmark tests of first- and second-row molecules and for transition metal systems. Modeling aspects of the protein metal complexes are discussed regarding both the size of the model being treated quantum mechanically and the treatment of the protein surrounding it. To illustrate the effects, structures computed without the effects of the protein are compared with experimental structures from enzymes, and results from simple dielectric models of the protein for electron transfer processes are described. The choice of spin state is discussed for multimetal complexes. Examples of mechanisms studied recently by density functional theory are described, such as O2 and methane activation in methane monooxygenase and O2 formation in photosystem II.

Journal Article↗

PubMed2006

Characterization of a catalytic ligand bridging metal ions in phosphodiesterases 4 and 5 by molecular dynamics simulations and hybrid quantum mechanical/molecular mechanical calculations.

Cyclic nucleotide phosphodiesterases (PDEs) constitute a large superfamily of enzymes regulating concentrations of intracellular second messengers cAMP and cGMP through PDE-catalyzed hydrolysis. Although three-dimensional x-ray crystal structures of PDE4 and PDE5 have been reported, it is uncertain whether a critical, second bridging ligand (BL2) in the active site is H2O or HO- because hydrogen atoms cannot be determined by x-ray diffraction. The identity of BL2 is theoretically determined by performing molecular dynamics simulations and hybrid quantum mechanical/molecular mechanical (QM/MM) calculations, for the first time, on the protein structures resolved by x-ray diffraction. The computational results confirm our previous suggestion, which was based on QM calculations on a simplified active site model, that BL2 in PDE4 should be HO-, rather than H2O, serving as the nucleophile to initialize the catalytic hydrolysis of cAMP. The molecular dynamics simulations and QM/MM calculations on PDE5 demonstrate for the first time that the BL2 in PDE5 should also be HO- rather than H2O as proposed in recently published reports on the x-ray crystal structures, which serves as the nucleophile to initialize the PDE5-catalyzed hydrolysis of cGMP. These fundamental structural insights provide a rational basis for future structure-based drug design targeting PDEs.

3',5'-Cyclic-AMP Phosphodiesterases↗

PubMed1981

Partial structural characterization of the cytoplasmic domain of the erythrocyte membrane protein, band 3.

The cytoplasmic domain of band 3 was released from spectrin-depleted, acetic acid-stripped erythrocyte membrane vesicles by mild chymotryptic digestion. After purification by ion exchange and gel filtration chromatography, the fragment preparation was found to be greater than 90% pure on polyacrylamide disc gels in the presence of 0.2% sodium dodecyl sulfate. The subunit Mr from the electrophoretic procedure was estimated at approximately 40,000. The isolated cytoplasmic fragment ws judged to be a dimer, since (i) the unmodified fragment and its disulfide-cross-linked (dimeric) counterpart eluted in the same peak fraction from a Sephacryl S-200 gel filtration column, and (ii) the sedimentation velocity molecular weight of the native fragment was calculated to be approximately 95,000. No evidence of either larger or smaller aggregates was obtained. The frictional ratio of the fragment was measured at 1.6, suggesting a highly elongated morphology. The circular dichroism spectrum of the fragment corresponded to approximately 37% alpha helix. Titration of the cytoplasmic fragment over the physiological pH range gave rise to a reversible 2-fold increase in the intrinsic fluorescence quantum yield (lambda ex, 290 nm; lambda em, 335 nm) between pH 6 and 9. Computer analysis of the data yielded a temperature-dependent apparent pKa of 7.8 at 37 degrees C and 8.1 at 20 degrees C, both with Hill coefficients less than or equal to 1. Calorimetric experiments revealed a similar sensitivity to pH, where the denaturation temperature of the fragment titrated from 74 degrees C at pH 6 to 59 degrees C at pH 8.5, with an apparent pKa of 7.3 and a Hill coefficient less than 1. The enthalpies and widths at half-height of the transitions were also exquisitely sensitive to pH. The fluorescence and calorimetric data could all be described by the titration of a single ionizable group of apparent pKa of 7.8 at 37 degrees C and delta pKa/degrees C of -0.018. The ionization of this critical group is suggested to exert significant control over the structure/stability of the cytoplasmic domain of band 3.

Amino Acids↗

PubMed2006

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↗

PubMed2006

Solid-state NMR, crystallographic, and computational investigation of bisphosphonates and farnesyl diphosphate synthase-bisphosphonate complexes.

Bisphosphonates are a class of molecules in widespread use in treating bone resorption diseases and are also of interest as immunomodulators and anti-infectives. They function by inhibiting the enzyme farnesyl diphosphate synthase (FPPS), but the details of how these molecules bind are not fully understood. Here, we report the results of a solid-state (13)C, (15)N, and (31)P magic-angle sample spinning (MAS) NMR and quantum chemical investigation of several bisphosphonates, both as pure compounds and when bound to FPPS, to provide information about side-chain and phosphonate backbone protonation states when bound to the enzyme. We then used computational docking methods (with the charges assigned by NMR) to predict how several bisphosphonates bind to FPPS. Finally, we used X-ray crystallography to determine the structures of two potent bisphosphonate inhibitors, finding good agreement with the computational results, opening up the possibility of using the combination of NMR, quantum chemistry and molecular docking to facilitate the design of other, novel prenytransferase inhibitors.

Crystallography, X-Ray↗

PubMed1985

Electron density calculations as an extension of protein structure refinement. Streptomyces griseus protease A at 1.5 A resolution.

Ab initio quantum mechanical calculations have been used to obtain details of the electron density distribution in a high-resolution refined protein structure. It is shown that with accurate atomic co-ordinates, electron density may be calculated with a quality similar to that which can be obtained directly from crystallographic studies of small organic molecules, and that this density contains information relevant to the understanding of catalysis. Atomic co-ordinates from the 1.8 A and 1.5 A resolution refinements of the crystal structure of protease A from Streptomyces griseus have been used to examine the influence of the environment on the electron density in the side-chain of the active site histidine (His57). The neighbouring aspartic acid 102 is the dominant factor in the environment, and quantum mechanical calculations have been performed on these two residues. Most interesting from the point of view of understanding the catalytic process is the effect that Asp102 has on the electron density in the region of the imidazole nitrogen (N epsilon 2) adjacent to the active site serine 195. In the positively charged imidazolium species, there is a polarization of the N epsilon 2-H bond, reducing the bonding density in a manner that may lower the height of the energy barrier for proton transfer. In the uncharged imidazole species, the proximity of Asp102 causes a movement of density from the lone pair region of the N epsilon 2 into the pi bonding region above and below the plane of the ring. Although it is shown that the primary effect of the aspartic acid is electrostatic, this movement is perpendicular to the direction of the electric field inducing it.

Amino Acid Sequence↗