Adrian E. Roitberg

Comparison of multiple Amber force fields and development of improved protein backbone parameters.

The ff94 force field that is commonly associated with the Amber simulation package is one of the most widely used parameter sets for biomolecular simulation. After a decade of extensive use and testing, limitations in this force field, such as over‐stabilization of α‐helices, were reported by us and other researchers. This led to a number of attempts to improve these parameters, resulting in a variety of “Amber” force fields and significant difficulty in determining which should be used for a particular application. We show that several of these continue to suffer from inadequate balance between different secondary structure elements. In addition, the approach used in most of these studies neglected to account for the existence in Amber of two sets of backbone φ/ψ dihedral terms. This led to parameter sets that provide unreasonable conformational preferences for glycine. We report here an effort to improve the φ/ψ dihedral terms in the ff99 energy function. Dihedral term parameters are based on fitting the energies of multiple conformations of glycine and alanine tetrapeptides from high level ab initio quantum mechanical calculations. The new parameters for backbone dihedrals replace those in the existing ff99 force field. This parameter set, which we denote ff99SB, achieves a better balance of secondary structure elements as judged by improved distribution of backbone dihedrals for glycine and alanine with respect to PDB survey data. It also accomplishes improved agreement with published experimental data for conformational preferences of short alanine peptides and better accord with experimental NMR relaxation data of test protein systems. Proteins 2006.

MMPBSA.py: An Efficient Program for End-State Free Energy Calculations

MM-PBSA is a post-processing end-state method to calculate free energies of molecules in solution. MMPBSA.py is a program written in Python for streamlining end-state free energy calculations using ensembles derived from molecular dynamics (MD) or Monte Carlo (MC) simulations. Several implicit solvation models are available with MMPBSA.py, including the Poisson-Boltzmann Model, the Generalized Born Model, and the Reference Interaction Site Model. Vibrational frequencies may be calculated using normal mode or quasi-harmonic analysis to approximate the solute entropy. Specific interactions can also be dissected using free energy decomposition or alanine scanning. A parallel implementation significantly speeds up the calculation by dividing frames evenly across available processors. MMPBSA.py is an efficient, user-friendly program with the flexibility to accommodate the needs of users performing end-state free energy calculations. The source code can be downloaded at http://ambermd.org/ with AmberTools, released under the GNU General Public License.

Pulsed terahertz spectroscopy of DNA, bovine serum albumin and collagen between 0.1 and 2.0 THz

We report the first use of pulsed terahertz spectroscopy to examine low-frequency collective vibrational modes of biomolecules. Broadband absorption increasing with frequency was observed for lyophilized powder samples of calf thymus DNA, bovine serum albumin and collagen in the 0.06–2.00 THz (2–67 cm−1) frequency range, suggesting that a large number of the low-frequency collective modes for these systems are IR active. Transmission measurements at room temperature showed increasing FIR absorption with hydration and denaturing.

Current‐voltage characteristics of molecular wires: Eigenvalue staircase, Coulomb blockade, and rectification

We have studied the current vs voltage curves (I–V characteristics) of a mesoscopic device consisting of two electrodes and a molecular wire. The wire Hamiltonian includes both electronic tunneling and Coulomb repulsion within a Hubbard model that is treated at the Hartree–Fock level. The inclusion of electron repulsion is an extension of our previous work that only considered the case of noninteracting electrons. We have found several important features in the calculated characteristics of the wire. These include (1) a staircaselike structure that strongly resembles that associated with Coulomb blockade in heterostructures and quantum dots, but that in the case of the wire is associated with the discrete nature of the molecular resonances; (2) regions of negative differential resistance associated with increased localization of the molecular resonances. Our theoretical model includes a consistent treatment of the conduction in the linear and nonlinear regimes which remains valid even when the device is o...

The injecting energy at molecule/metal interfaces: Implications for conductance of molecular junctions from an ab initio molecular description

To study the electronic transport of molecular wire circuits, we present a time-independent scattering formalism which includes an ab initio description of the molecular electronic structure. This allows us to obtain the molecule–metal coupling description at the same level of theory. The conductance of junction α, α′ xylyl dithiol and benzene-1,4-dithiol between gold electrodes is obtained and compared with available experimental data. The conductance depends dramatically on the relative position of the Fermi energy of the metal with respect to the molecular levels. We obtain an estimate for the injecting energy of the electron onto the molecule by varying the distance between the molecule and the attached gold clusters. Contrary to the standard assumption, we find that the injecting energy lies close to the molecular highest occupied molecular orbital, rather than in the middle of the gap; it is just the work function of the bulk metal. Finally, the adequacy of the widely used extended Huckel method for...

Modeling side chains in peptides and proteins: Application of the locally enhanced sampling and the simulated annealing methods to find minimum energy conformations

A new optimization protocol is proposed which is based on a combination of a mean field approximation and simulated annealing. Instead of optimizing the energy of the real system the energy of a new mean field system is minimized. The global minimum of the new system and the original system is the same. The mean‐field optimization is advantageous to the optimization of the real system since (a) More statistics are obtained for alternative solutions and (b) the barrier heights separating the minima are reduced compared to the real system. Computational examples are provided for placement of side chains in tetrapeptides and in a small protein BPTI.

MOIL: A program for simulations of macromolecules

Abstract A package of computer programs for molecular dynamics simulations-MOIL-is described. A flexible data structure enables the study of macromolecules with potentials consistent with the AMBER/OPLS force field. The supplied parameter set has proteins in mind. In addition to ‘wide spread’ applications such as energy, energy minimization, normal modes, dynamics and free energy calculations code is also provided to pursue less common applications. This includes reaction path calculations (in condensed phases), uses of the mean field approach for enhanced sampling (LES-locally enhanced sampling) and calculations of curve crossing using the Landau-Zener model. A brief review of the overall program is provided. A few modules are discussed in considerable detail.

Molecular wire conductance: Electrostatic potential spatial profile

We have studied the effect of the electrostatic potential on the current across a one-dimensional tight-binding molecular wire by solving self-consistently the Poisson and Schrodinger equations. The results indicate that electrostatic effects on the current are very important in the nonlinear regime. They manifest themselves through a strong variation of the voltage drop in the interfacial region compared to the linear ramp expected in the absence of charge in the wire and also in the nature of the current–voltage characteristics.

Nonadiabatic Excited-State Molecular Dynamics Modeling of Photoinduced Dynamics in Conjugated Molecules

Nonadiabatic dynamics generally defines the entire evolution of electronic excitations in optically active molecular materials. It is commonly associated with a number of fundamental and complex processes such as intraband relaxation, energy transfer, and light harvesting influenced by the spatial evolution of excitations and transformation of photoexcitation energy into electrical energy via charge separation (e.g., charge injection at interfaces). To treat ultrafast excited-state dynamics and exciton/charge transport we have developed a nonadiabatic excited-state molecular dynamics (NA-ESMD) framework incorporating quantum transitions. Our calculations rely on the use of the Collective Electronic Oscillator (CEO) package accounting for many-body effects and actual potential energy surfaces of the excited states combined with Tullys fewest switches algorithm for surface hopping for probing nonadiabatic processes. This method is applied to model the photoinduced dynamics of distyrylbenzene (a small oligomer of polyphenylene vinylene, PPV). Our analysis shows intricate details of photoinduced vibronic relaxation and identifies specific slow and fast nuclear motions that are strongly coupled to the electronic degrees of freedom, namely, torsion and bond length alternation, respectively. Nonadiabatic relaxation of the highly excited mA(g) state is predicted to occur on a femtosecond time scale at room temperature and on a picosecond time scale at low temperature.

Long-Time-Step Molecular Dynamics through Hydrogen Mass Repartitioning.

Previous studies have shown that the method of hydrogen mass repartitioning (HMR) is a potentially useful tool for accelerating molecular dynamics (MD) simulations. By repartitioning the mass of heavy atoms into the bonded hydrogen atoms, it is possible to slow the highest-frequency motions of the macromolecule under study, thus allowing the time step of the simulation to be increased by up to a factor of 2. In this communication, we investigate further how this mass repartitioning allows the simulation time step to be increased in a stable fashion without significantly increasing discretization error. To this end, we ran a set of simulations with different time steps and mass distributions on a three-residue peptide to get a comprehensive view of the effect of mass repartitioning and time step increase on a system whose accessible phase space is fully explored in a relatively short amount of time. We next studied a 129-residue protein, hen egg white lysozyme (HEWL), to verify that the observed behavior extends to a larger, more-realistic, system. Results for the protein include structural comparisons from MD trajectories, as well as comparisons of pKa calculations via constant-pH MD. We also calculated a potential of mean force (PMF) of a dihedral rotation for the MTS [(1-oxyl-2,2,5,5-tetramethyl-pyrroline-3-methyl)methanethiosulfonate] spin label via umbrella sampling with a set of regular MD trajectories, as well as a set of mass-repartitioned trajectories with a time step of 4 fs. Since no significant difference in kinetics or thermodynamics is observed by the use of fast HMR trajectories, further evidence is provided that long-time-step HMR MD simulations are a viable tool for accelerating MD simulations for molecules of biochemical interest.